Cytosine, but not adenine, base editors induce genome-wide off-target mutations in rice

The Sequence Alignment/Map format and SAMtools

Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041 · see citing works

Fast and accurate short read alignment with Burrows-Wheeler transform

Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607 · see citing works

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., et al. (2010) · Genome Research · doi:10.1101/gr.107524.110 · Cited by 27,895 · see citing works

BEDTools: a flexible suite of utilities for comparing genomic features

Quinlan, A. R., & Hall, I. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq033 · Cited by 27,437 · see citing works

HISAT: a fast spliced aligner with low memory requirements

Kim, D., Langmead, B., & Salzberg, S. L. (2015) · Nature Methods · doi:10.1038/nmeth.3317 · Cited by 24,112 · see citing works

Fast and accurate long-read alignment with Burrows-Wheeler transform.

Li, H., & Durbin, R. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btp698 · Cited by 12,063 · see citing works

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w ¹¹¹⁸ ; iso-2; iso-3

Cingolani, P., Platts, A., Wang, L. L., Coon, M., Nguyen, T., Wang, L., Land, S. J., Lu, X., & Ruden, D. M. (2012) · Fly · doi:10.4161/fly.19695 · Cited by 11,816 · see citing works

Circos: An information aesthetic for comparative genomicsPreprint

Krzywinski, M. I., Schein, J. E., Birol, İ., Connors, J. M., Gascoyne, R. D., Horsman, D. E., Jones, S. J. M., & Marra, M. A. (2009) · Genome Research · doi:10.1101/gr.092759.109 · Cited by 10,838 · see citing works

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

Thorvaldsdottir, H., Robinson, J. T., & Mesirov, J. P. (2013) · Briefings in Bioinformatics · doi:10.1093/bib/bbs017 · Cited by 9,049 · see citing works

Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage

Komor, A. C., Kim, Y. B., Packer, M. S., Zuris, J. A., & Liu, D. R. (2016) · Nature · doi:10.1038/nature17946 · Cited by 5,437 · see citing works

Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage

Gaudelli, N. M., Komor, A. C., Rees, H. A., Packer, M. S., Badran, A. H., Bryson, D. I., & Liu, D. R. (2017) · Nature · doi:10.1038/nature24644 · Cited by 4,184 · see citing works

VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R

Chen, H., & Boutros, P. C. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-35 · Cited by 3,150 · see citing works

ClinVar: public archive of interpretations of clinically relevant variants

Landrum, M. J., Lee, J. M., Benson, M., Brown, G., Chao, C., Chitipiralla, S., Gu, B., Hart, J., Hoffman, D., Hoover, J., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1222 · Cited by 2,758 · see citing works

Cas-OFFinder: A fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases

Bae, S., Park, J., & Kim, J.-S. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu048 · Cited by 2,339 · see citing works

Base editing: precision chemistry on the genome and transcriptome of living cells

Rees, H. A., & Liu, D. R. (2018) · Nature Reviews Genetics · doi:10.1038/s41576-018-0059-1 · Cited by 1,675 · see citing works

Strelka2: fast and accurate calling of germline and somatic variants

Kim, S., Scheffler, K., Halpern, A. L., Bekritsky, M. A., Noh, E., Källberg, M., Chen, X., Kim, Y., Beyter, D., Krusche, P., et al. (2018) · Nature Methods · doi:10.1038/s41592-018-0051-x · Cited by 1,643 · see citing works

Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems

Nishida, K., Arazoe, T., Yachie, N., Banno, S., Kakimoto, M., Tabata, M., Mochizuki, M., Miyabe, A., Araki, M., Hara, K. Y., et al. (2016) · Science · doi:10.1126/science.aaf8729 · Cited by 1,349 · see citing works

LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets

Wilm, A., Aw, P. P. K., Bertrand, D., Yeo, G. H. T., Ong, S. H., Wong, C. H., Khor, C. C., Petric, R., Hibberd, M. L., & Nagarajan, N. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks918 · Cited by 1,338 · see citing works

Precise base editing in rice, wheat and maize with a Cas9-cytidine deaminase fusion

Zong, Y., Wang, Y., Li, C., Zhang, R., Chen, K., Ran, Y., Qiu, J., Wang, D., & Gao, C. (2017) · Nature Biotechnology · doi:10.1038/nbt.3811 · Cited by 875 · see citing works

Cytosine base editor generates substantial off-target single-nucleotide variants in mouse embryos

Zuo, E., Sun, Y., Wei, W., Yuan, T., Ying, W., Sun, H., Yuan, L., Steinmetz, L. M., Li, Y., & Yang, H. (2019) · Science · doi:10.1126/science.aav9973 · Cited by 782 · see citing works

Increasing the genome-targeting scope and precision of base editing with engineered Cas9-cytidine deaminase fusions

Kim, Y. B., Komor, A. C., Levy, J. M., Packer, M. S., Zhao, K. T., & Liu, D. R. (2017) · Nature Biotechnology · doi:10.1038/nbt.3803 · Cited by 756 · see citing works

RNA Editing Enzyme APOBEC1 and Some of Its Homologs Can Act as DNA Mutators

Harris, R. S., Petersen‐Mahrt, S. K., & Neuberger, M. S. (2002) · Molecular Cell · doi:10.1016/s1097-2765(02)00742-6 · Cited by 604 · see citing works

Expanded base editing in rice and wheat using a Cas9-adenosine deaminase fusion

Li, C., Zong, Y., Wang, Y., Jin, S., Zhang, D., Song, Q., Zhang, R., & Gao, C. (2018) · Genome biology · doi:10.1186/s13059-018-1443-z · Cited by 499 · see citing works

An APOBEC3A-Cas9 base editor with minimized bystander and off-target activities

Gehrke, J. M., Cervantes, O., Clement, K., Wu, Y., Zeng, J., Bauer, D. E., Pinello, L., & Joung, J. K. (2018) · Nature Biotechnology · doi:10.1038/nbt.4199 · Cited by 433 · see citing works

Improving the DNA specificity and applicability of base editing through protein engineering and protein delivery

Rees, H. A., Komor, A. C., Yeh, W.-H., Caetano‐Lopes, J., Warman, M. L., Edge, A. S. B., & Liu, D. R. (2017) · Nature Communications · doi:10.1038/ncomms15790 · Cited by 422 · see citing works

Single-Nucleotide Mutations for Plant Functional Genomics

Henikoff, S., & Comai, L. (2003) · Annual Review of Plant Biology · doi:10.1146/annurev.arplant.54.031902.135009 · Cited by 325 · see citing works

Evolution and diversification of lamprey antigen receptors: evidence for involvement of an AID-APOBEC family cytosine deaminase

Rogozin, I. B., Iyer, L. M., Liang, L., Glazko, G. V., Liston, V. G., Pavlov, Y. I., Aravind, L., & Pancer, Z. (2007) · Nature Immunology · doi:10.1038/ni1463 · Cited by 311 · see citing works

Rapid and Efficient Gene Modification in Rice and Brachypodium Using TALENs

Shan, Q., Wang, Y., Chen, K., Liang, Z., Li, J., Zhang, Y., Zhang, K., Liu, J., Voytas, D. F., Zheng, X., et al. (2013) · Molecular Plant · doi:10.1093/mp/sss162 · Cited by 288 · see citing works

Genome-wide target specificities of CRISPR RNA-guided programmable deaminases

Kim, D., Lim, K., Kim, S., Yoon, S.-H., Kim, K., Ryu, S.-M., & Kim, J. (2017) · Nature Biotechnology · doi:10.1038/nbt.3852 · Cited by 275 · see citing works

MiR408 Regulates Grain Yield and Photosynthesis via a Phytocyanin Protein

Zhang, J., Yu, Y., Feng, Y., Zhou, Y.-F., Zhang, F., Yang, Y., Lei, M.-Q., Zhang, Y., & Chen, Y.-Q. (2017) · PLANT PHYSIOLOGY · doi:10.1104/pp.17.01169 · Cited by 174 · see citing works

Genome-wide profiling of adenine base editor specificity by EndoV-seq

Liang, P., Xie, X., Zhi, S., Sun, H., Zhang, X., Chen, Y., Chen, Y., Xiong, Y., Ma, W., Liu, D., et al. (2019) · Nature Communications · doi:10.1038/s41467-018-07988-z · Cited by 148 · see citing works

Targeting fidelity of adenine and cytosine base editors in mouse embryos

Lee, H., Willi, M., Miller, S. M., Kim, S., Liu, C., Liu, D. R., & Hennighausen, L. G. (2018) · Nature Communications · doi:10.1038/s41467-018-07322-7 · Cited by 82 · see citing works

Stress responsive miR-31 is a major modulator of mouse intestinal stem cells during regeneration and tumorigenesis

Tian, Y., Ma, X., Lv, C., Sheng, X., Li, X., Zhao, R., Song, Y., Andl, T., Plikus, M. V., Sun, J., et al. (2017) · eLife · doi:10.7554/elife.29538 · Cited by 69 · see citing works

Increased spontaneous mutation frequency in human cells expressing the phage PBS2-encoded inhibitor of uracil-DNA glycosylase

Radany, E. H., Dornfeld, K. J., Sanderson, R. J., Savage, M. K., Majumdar, A., Seidman, M. M., & Mosbaugh, D. W. (2000) · Mutation Research/DNA Repair · doi:10.1016/s0921-8777(00)00040-9 · Cited by 41 · see citing works

Genome editing with CRISPR–Cas nucleases, base editors, transposases and prime editors

Anzalone, A. V., Koblan, L. W., & Liu, D. R. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0561-9 · Cited by 2,237 · see citing works

The next generation of CRISPR–Cas technologies and applications

Pickar-Oliver, A., & Gersbach, C. A. (2019) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-019-0131-5 · Cited by 1,459 · see citing works

Genome engineering for crop improvement and future agriculture

Gao, C. (2021) · Cell · doi:10.1016/j.cell.2021.01.005 · Cited by 1,037 · see citing works

Cytosine base editor generates substantial off-target single-nucleotide variants in mouse embryos

Zuo, E., Sun, Y., Wei, W., Yuan, T., Ying, W., Sun, H., Yuan, L., Steinmetz, L. M., Li, Y., & Yang, H. (2019) · Science · doi:10.1126/science.aav9973 · Cited by 782 · see citing works

Off-target effects in CRISPR/Cas9 gene editing

Guo, C., Ma, X., Gao, F., & Guo, Y. (2023) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2023.1143157 · Cited by 625 · see citing works

Lineage tracing meets single-cell omics: opportunities and challenges

Wagner, D. E., & Klein, A. M. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-020-0223-2 · Cited by 594 · see citing works

Prime editing for precise and highly versatile genome manipulation

Chen, P. J., & Liu, D. R. (2022) · Nature Reviews Genetics · doi:10.1038/s41576-022-00541-1 · Cited by 621 · see citing works

Directed evolution of adenine base editors with increased activity and therapeutic application

Gaudelli, N. M., Lam, D. K., Rees, H. A., Solá-Esteves, N. M., Barrera, L. A., Born, D. A., Edwards, A., Gehrke, J. M., Lee, S., Liquori, A., et al. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0491-6 · Cited by 518 · see citing works

Off-target RNA mutation induced by DNA base editing and its elimination by mutagenesis

Zhou, C., Sun, Y., Yan, R., Liu, Y., Zuo, E., Gu, C., Han, L., Wei, Y., Hu, X., Zeng, R., et al. (2019) · Nature · doi:10.1038/s41586-019-1314-0 · Cited by 482 · see citing works

Evaluation and minimization of Cas9-independent off-target DNA editing by cytosine base editors

Doman, J. L., Raguram, A., Newby, G. A., & Liu, D. R. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0414-6 · Cited by 473 · see citing works

Base editing: advances and therapeutic opportunities

Porto, E. M., Komor, A. C., Slaymaker, I. M., & Yeo, G. W.-M. (2020) · Nature Reviews Drug Discovery · doi:10.1038/s41573-020-0084-6 · Cited by 475 · see citing works

A cytosine deaminase for programmable single-base RNA editing

Abudayyeh, O. O., Gootenberg, J. S., Franklin, B., Koob, J. G., Kellner, M. J., Ladha, A., Joung, J., Kirchgatterer, P. C., Cox, D. B. T., & Zhang, F. (2019) · Science · doi:10.1126/science.aax7063 · Cited by 456 · see citing works

Latest Developed Strategies to Minimize the Off-Target Effects in CRISPR-Cas-Mediated Genome Editing

Naeem, M., Majeed, S., Hoque, M. Z., & Ahmad, I. (2020) · Cells · doi:10.3390/cells9071608 · Cited by 457 · see citing works

Targeted, random mutagenesis of plant genes with dual cytosine and adenine base editors

Li, C., Zhang, R., Meng, X., Chen, S., Zong, Y., Lu, C., Qiu, J., Chen, Y., Li, J., & Gao, C. (2020) · Nature Biotechnology · doi:10.1038/s41587-019-0393-7 · Cited by 410 · see citing works

Precise plant genome editing using base editors and prime editors

Molla, K. A., Sretenovic, S., Bansal, K. C., & Qi, Y. (2021) · Nature Plants · doi:10.1038/s41477-021-00991-1 · Cited by 387 · see citing works

The emerging and uncultivated potential of CRISPR technology in plant science

Zhang, Y., Malzahn, A. A., Sretenovic, S., & Qi, Y. (2019) · Nature Plants · doi:10.1038/s41477-019-0461-5 · Cited by 404 · see citing works

In vivo adenine base editing of PCSK9 in macaques reduces LDL cholesterol levels

Rothgangl, T., Dennis, M. K., Lin, P. J. C., Oka, R., Witzigmann, D., Villiger, L., Qi, W., Hruzova, M., Kissling, L., Lenggenhager, D., et al. (2021) · Nature Biotechnology · doi:10.1038/s41587-021-00933-4 · Cited by 378 · see citing works

CRISPR/Cas Systems in Genome Editing: Methodologies and Tools for sgRNA Design, Off‐Target Evaluation, and Strategies to Mitigate Off‐Target Effects

Manghwar, H., Li, B., Ding, X. L., Hussain, A., Lindsey, K., Zhang, X., & Jin, S. (2020) · Advanced Science · doi:10.1002/advs.201902312 · Cited by 394 · see citing works

Continuous evolution of SpCas9 variants compatible with non-G PAMs

Miller, S. M., Wang, T., Randolph, P. B., Arbab, M., Shen, M. W., Huang, T. P., Matuszek, Ż., Newby, G. A., Rees, H. A., & Liu, D. R. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0412-8 · Cited by 347 · see citing works

CRISPR/Cas-Mediated Base Editing: Technical Considerations and Practical Applications

Molla, K. A., & Yang, Y. (2019) · Trends in biotechnology · doi:10.1016/j.tibtech.2019.03.008 · Cited by 336 · see citing works

Analysis and minimization of cellular RNA editing by DNA adenine base editors

Rees, H. A., Wilson, C., Doman, J. L., & Liu, D. R. (2019) · Science Advances · doi:10.1126/sciadv.aax5717 · Cited by 278 · see citing works

Programmable RNA editing by recruiting endogenous ADAR using engineered RNAs

Qu, L., Yi, Z., Zhu, S., Wang, C., Cao, Z., Zhou, Z. L., Yuan, P., Yu, Y. F., Tian, F., Liu, Z., et al. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0178-z · Cited by 287 · see citing works

Next-generation stem cells — ushering in a new era of cell-based therapies

Kimbrel, E. A., & Lanza, R. (2020) · Nature Reviews Drug Discovery · doi:10.1038/s41573-020-0064-x · Cited by 280 · see citing works

Evolution of an adenine base editor into a small, efficient cytosine base editor with low off-target activity

Neugebauer, M. E., Hsu, A., Arbab, M., Krasnow, N. A., McElroy, A. N., Pandey, S., Doman, J. L., Huang, T. P., Raguram, A., Banskota, S., et al. (2022) · Nature Biotechnology · doi:10.1038/s41587-022-01533-6 · Cited by 273 · see citing works

Dual base editor catalyzes both cytosine and adenine base conversions in human cells

Zhang, X., Zhu, B., Chen, L., Xie, L., Yu, W., Wang, Y., Li, L., Yin, S., Yang, L., Hu, H., et al. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0527-y · Cited by 270 · see citing works

Precision genome editing in plants: state-of-the-art in CRISPR/Cas9-based genome engineering

Wada, N., Ueta, R., Osakabe, Y., & Osakabe, K. (2020) · BMC Plant Biology · doi:10.1186/s12870-020-02385-5 · Cited by 271 · see citing works

CRISPR technologies for genome, epigenome and transcriptome editing

Villiger, L., Joung, J., Koblan, L. W., Weissman, J. S., Abudayyeh, O. O., & Gootenberg, J. S. (2024) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-023-00697-6 · Cited by 264 · see citing works

Delivery of CRISPR-Cas tools for in vivo genome editing therapy: Trends and challenges

Taha, E. A., Lee, J., & Hotta, A. (2022) · Journal of Controlled Release · doi:10.1016/j.jconrel.2022.01.013 · Cited by 259 · see citing works

Anti-CRISPR protein applications: natural brakes for CRISPR-Cas technologies

Marino, N. D., Pinilla‐Redondo, R., Csörgő, B., & Bondy‐Denomy, J. (2020) · Nature Methods · doi:10.1038/s41592-020-0771-6 · Cited by 240 · see citing works

Precise correction of Duchenne muscular dystrophy exon deletion mutations by base and prime editing

Chemello, F., Chai, A. C., Li, H. Z., Rodríguez-Caycedo, C., Sanchez‐Ortiz, E., Atmanli, A., Mireault, A. A., Liu, N., Bassel‐Duby, R., & Olson, E. N. (2021) · Science Advances · doi:10.1126/sciadv.abg4910 · Cited by 250 · see citing works

Venn diagrams in bioinformatics

Jia, A., Xu, L., & Wang, Y. (2021) · Briefings in Bioinformatics · doi:10.1093/bib/bbab108 · Cited by 243 · see citing works

Discovery of deaminase functions by structure-based protein clustering

(2023) · doi:10.1016/j.cell.2023.05.041 · Cited by 240 · see citing works

Highly efficient multiplex human T cell engineering without double-strand breaks using Cas9 base editors

Webber, B. R., Lonetree, C.-L., Kluesner, M. G., Johnson, M. J., Pomeroy, E. J., Diers, M. D., Lahr, W. S., Draper, G. M., Slipek, N. J., Smeester, B. A., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-13007-6 · Cited by 232 · see citing works

Base editing in crops: current advances, limitations and future implications

Mishra, R., Joshi, R. K., & Zhao, K. (2019) · Plant Biotechnology Journal · doi:10.1111/pbi.13225 · Cited by 231 · see citing works

Treatment of a Mouse Model of ALS by In Vivo Base Editing

Lim, C. K. W., Gapinske, M., Brooks, A. K., Woods, W. S., Powell, J. E., C., M. A. Z., Winter, J., Pérez‐Piñera, P., & Gaj, T. (2020) · Molecular Therapy · doi:10.1016/j.ymthe.2020.01.005 · Cited by 225 · see citing works

CRISPR-Based Adenine Editors Correct Nonsense Mutations in a Cystic Fibrosis Organoid Biobank

Geurts, M. H., de Poel, E., Amatngalim, G. D., Oka, R., Meijers, F. M., Kruisselbrink, E., van Mourik, P., Berkers, G., de Winter-de Groot, K. M., Michel, S., et al. (2020) · Cell Stem Cell · doi:10.1016/j.stem.2020.01.019 · Cited by 222 · see citing works

In Vivo AAV-CRISPR/Cas9–Mediated Gene Editing Ameliorates Atherosclerosis in Familial Hypercholesterolemia

Zhao, H., Li, Y., He, L., Pu, W., Yu, W., Li, Y., Wu, Y., Xu, C., Wei, Y., Ding, Q., et al. (2019) · Circulation · doi:10.1161/circulationaha.119.042476 · Cited by 212 · see citing works

Assessing and advancing the safety of CRISPR-Cas tools: from DNA to RNA editing

Tao, J., Bauer, D. E., & Chiarle, R. (2023) · Nature Communications · doi:10.1038/s41467-023-35886-6 · Cited by 215 · see citing works

Highly efficient DSB-free base editing for streptomycetes with CRISPR-BEST

Tong, Y., Whitford, C. M., Robertsen, H. L., Blin, K., Jørgensen, T. S., Klitgaard, A., Gren, T., Jiang, X., Weber, T., & Lee, S. Y. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1913493116 · Cited by 201 · see citing works

Engineered materials for in vivo delivery of genome-editing machinery

Tong, S., Moyo, B., Lee, C. M., Leong, K. W., & Bao, G. (2019) · Nature Reviews Materials · doi:10.1038/s41578-019-0145-9 · Cited by 206 · see citing works

Recent advances in the CRISPR genome editing tool set

Moon, S. B., Kim, D. Y., Ko, J., & Kim, Y.-S. (2019) · Experimental & Molecular Medicine · doi:10.1038/s12276-019-0339-7 · Cited by 208 · see citing works

Engineering a precise adenine base editor with minimal bystander editing

Chen, L., Zhang, S., Xue, N., Hong, M., Zhang, X., Zhang, D., Yang, J., Bai, S., Huang, Y., Meng, H., et al. (2023) · Nature Chemical Biology · doi:10.1038/s41589-022-01163-8 · Cited by 202 · see citing works

In vivo somatic cell base editing and prime editing

Newby, G. A., & Liu, D. R. (2021) · Molecular Therapy · doi:10.1016/j.ymthe.2021.09.002 · Cited by 192 · see citing works

Cytosine base editors with minimized unguided DNA and RNA off-target events and high on-target activity

Yu, Y., Leete, T., Born, D. A., Young, L., Barrera, L. A., Lee, S., Rees, H. A., Ciaramella, G., & Gaudelli, N. M. (2020) · Nature Communications · doi:10.1038/s41467-020-15887-5 · Cited by 190 · see citing works

Gene editing and CRISPR in the clinic: current and future perspectives

Hirakawa, M. P., Krishnakumar, R., Timlin, J. A., Carney, J. P., & Butler, K. S. (2020) · Bioscience Reports · doi:10.1042/bsr20200127 · Cited by 197 · see citing works

CRISPR-Cas Tools and Their Application in Genetic Engineering of Human Stem Cells and Organoids

Hendriks, D. F. G., Clevers, H. C., & Artegiani, B. (2020) · Cell stem cell · doi:10.1016/j.stem.2020.10.014 · Cited by 196 · see citing works

Engineered circular ADAR-recruiting RNAs increase the efficiency and fidelity of RNA editing in vitro and in vivo

Yi, Z., Qu, L., Tang, H., Liu, Z., Liu, Y., Tian, F., Wang, C., Zhang, X., Feng, Z., Yu, Y. F., et al. (2022) · Nature Biotechnology · doi:10.1038/s41587-021-01180-3 · Cited by 185 · see citing works

In vivo base editing restores sensory transduction and transiently improves auditory function in a mouse model of recessive deafness

Yeh, W.-H., Shubina-Oleinik, O., Levy, J. M., Pan, B., Newby, G. A., Wornow, M., Burt, R., Chen, J. C., Holt, J. R., & Liu, D. R. (2020) · Science Translational Medicine · doi:10.1126/scitranslmed.aay9101 · Cited by 179 · see citing works

Development of CRISPR-Cas systems for genome editing and beyond

Zhang, F. (2019) · Quarterly Reviews of Biophysics · doi:10.1017/s0033583519000052 · Cited by 185 · see citing works

Fine-tuning sugar content in strawberry

Xing, S., Chen, K., Zhu, H., Zhang, R., Zhang, H., Li, B., & Gao, C. (2020) · Genome biology · doi:10.1186/s13059-020-02146-5 · Cited by 178 · see citing works

Rationally designed APOBEC3B cytosine base editors with improved specificity

Jin, S., Fei, H., Zhu, Z., Luo, Y., Liu, J., Gao, S., Zhang, F., Chen, Y.-H., Wang, Y., & Gao, C. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.07.005 · Cited by 159 · see citing works

Perspectives on the Application of Genome-Editing Technologies in Crop Breeding

Hua, K., Zhang, J., Botella, J. R., Ma, C., Kong, F., Liu, B., & Zhu, J. (2019) · Molecular Plant · doi:10.1016/j.molp.2019.06.009 · Cited by 170 · see citing works

Engineering source-sink relations by prime editing confers heat-stress resilience in tomato and rice

Lou, H. F., Li, S., Shi, Z., Zou, Y.-P., Zhang, Y., Huang, X., Yang, D., Yang, Y., Li, Z., & Cao, X. (2024) · Cell · doi:10.1016/j.cell.2024.11.005 · Cited by 167 · see citing works

Restoration of visual function in adult mice with an inherited retinal disease via adenine base editing

Suh, S., Choi, E. H., Leinonen, H., Foik, A. T., Newby, G. A., Yeh, W.-H., Dong, Z., Kiser, P. D., Lyon, D. C., Liu, D. R., et al. (2020) · Nature Biomedical Engineering · doi:10.1038/s41551-020-00632-6 · Cited by 162 · see citing works

Ex vivo prime editing of patient haematopoietic stem cells rescues sickle-cell disease phenotypes after engraftment in mice

Everette, K. A., Newby, G. A., Levine, R. M., Mayberry, K. D., Jang, Y., Mayuranathan, T., Nimmagadda, N., Dempsey, E., Li, Y., Bhoopalan, S. V., et al. (2023) · Nature Biomedical Engineering · doi:10.1038/s41551-023-01026-0 · Cited by 167 · see citing works

A rationally engineered cytosine base editor retains high on-target activity while reducing both DNA and RNA off-target effects

Zuo, E., Sun, Y., Yuan, T., He, B., Zhou, C., Ying, W., Liu, J., Wu, W., Zeng, R., Li, Y., et al. (2020) · Nature Methods · doi:10.1038/s41592-020-0832-x · Cited by 164 · see citing works

Re-engineering the adenine deaminase TadA-8e for efficient and specific CRISPR-based cytosine base editing

Chen, L., Zhu, B., Ru, G., Meng, H., Yan, Y., Hong, M., Zhang, D., Luan, C., Zhang, S., Wu, H., et al. (2023) · Nature Biotechnology · doi:10.1038/s41587-022-01532-7 · Cited by 156 · see citing works

CRISPR/Cas9 for development of disease resistance in plants: recent progress, limitations and future prospects

Ahmad, S., Wei, X., Sheng, Z., Hu, P., & Tang, S. (2019) · Briefings in Functional Genomics · doi:10.1093/bfgp/elz041 · Cited by 153 · see citing works

Current Status and Challenges of DNA Base Editing Tools

Jeong, Y. K., Song, B., & Bae, S. (2020) · Molecular Therapy · doi:10.1016/j.ymthe.2020.07.021 · Cited by 153 · see citing works

Improved plant cytosine base editors with high editing activity, purity, and specificity

Ren, Q., Sretenovic, S., Liu, G., Zhong, Z., Wang, J., Huang, L., Tang, X., Guo, Y., Liu, L., Wu, Y., et al. (2021) · Plant Biotechnology Journal · doi:10.1111/pbi.13635 · Cited by 131 · see citing works

Evaluating CRISPR-based prime editing for cancer modeling and CFTR repair in organoids

Geurts, M. H., de Poel, E., Pleguezuelos-Manzano, C., Oka, R., Carrillo, L., Andersson-Rolf, A., Boretto, M., Brunsveld, J. E., van Boxtel, R., Beekman, J. M., et al. (2021) · Life Science Alliance · doi:10.26508/lsa.202000940 · Cited by 151 · see citing works

Construct design for CRISPR/Cas-based genome editing in plants

Hassan, M. M., Zhang, Y., Yuan, G., De, K., Chen, J., Muchero, W., Tuskan, G. A., Qi, Y., & Yang, X. (2021) · Trends in Plant Science · doi:10.1016/j.tplants.2021.06.015 · Cited by 136 · see citing works

Adenine base editors catalyze cytosine conversions in human cells

Kim, H. S., Jeong, Y. K., Hur, J. K., Kim, J., & Bae, S. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0254-4 · Cited by 127 · see citing works

Improved cytosine base editors generated from TadA variants

Lam, D. K., Feliciano, P. R., Arif, A., Bohnuud, T., Fernandez, T. P., Gehrke, J. M., Grayson, P., Lee, K. D., Ortega, M. A., Sawyer, C. B., et al. (2023) · Nature Biotechnology · doi:10.1038/s41587-022-01611-9 · Cited by 138 · see citing works

CRISPR–Cas applications in agriculture and plant research

Tuncel, A., Pan, C., Clem, J. S., Liu, D., & Qi, Y. (2025) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-025-00834-3 · Cited by 139 · see citing works

Genome-wide specificity of prime editors in plants

Jin, S., Lin, Q., Luo, Y., Zhu, Z., Liu, G., Li, Y., Chen, K., Qiu, J., & Gao, C. (2021) · Nature Biotechnology · doi:10.1038/s41587-021-00891-x · Cited by 127 · see citing works

Mitochondrial base editor induces substantial nuclear off-target mutations

Lei, Z.-X., Meng, H., Liu, L., Zhao, H., Rao, X., Yan, Y., Wu, H., Liu, M., He, A., & Yi, C. (2022) · Nature · doi:10.1038/s41586-022-04836-5 · Cited by 118 · see citing works

The Solanum tuberosum GBSSI gene: a target for assessing gene and base editing in tetraploid potato

Veillet, F., Chauvin, L., Kermarrec, M.-P., Sevestre, F., Merrer, M., Terret, Z., Szydlowski, N., Devaux, P., Gallois, J.-L., & Chauvin, J.-E. (2019) · Plant Cell Reports · doi:10.1007/s00299-019-02426-w · Cited by 124 · see citing works

Genome editing for plant research and crop improvement

Zhan, X., Lu, Y., Zhu, J., & Botella, J. R. (2020) · Journal of Integrative Plant Biology · doi:10.1111/jipb.13063 · Cited by 121 · see citing works

Efficient base editing for multiple genes and loci in pigs using base editors

Xie, J., Ge, W., Li, N., Liu, Q., Chen, F., Yang, X., Huang, X., Ouyang, Z., Zhang, Q., Zhao, Y., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-10421-8 · Cited by 122 · see citing works

Efficient Generation and Correction of Mutations in Human iPS Cells Utilizing mRNAs of CRISPR Base Editors and Prime Editors

Sürün, D., Schneider, A., Mircetic, J., Neumann, K., Lansing, F., Paszkowski‐Rogacz, M., Hänchen, V., Lee‐Kirsch, M. A., & Buchholz, F. (2020) · Genes · doi:10.3390/genes11050511 · Cited by 121 · see citing works

Base editing in plants: Current status and challenges

Bharat, S. S., Li, S., Li, J., Yan, L., & Xia, L. (2019) · The Crop Journal · doi:10.1016/j.cj.2019.10.002 · Cited by 123 · see citing works

CRISPR Modeling and Correction of Cardiovascular Disease

Liu, N., & Olson, E. N. (2022) · Circulation Research · doi:10.1161/circresaha.122.320496 · Cited by 118 · see citing works

Brainwide silencing of prion protein by AAV-mediated delivery of an engineered compact epigenetic editor

Neumann, E. N., Bertozzi, T. M., Wu, E., Serack, F. E., Harvey, J. W., Brauer, P. P., Pirtle, C. P., Coffey, A. A., Howard, M., Kamath, N., et al. (2024) · Science · doi:10.1126/science.ado7082 · Cited by 120 · see citing works

Plant Genome Editing and the Relevance of Off-Target Changes

Graham, N. D., Patil, G., Bubeck, D. M., Dobert, R. C., Glenn, K. C., Gutsche, A. T., Kumar, S., Lindbo, J. A., Maas, L., May, G. D., et al. (2020) · PLANT PHYSIOLOGY · doi:10.1104/pp.19.01194 · Cited by 118 · see citing works

Target base editing in soybean using a modified CRISPR/Cas9 system

Cai, Y., Chen, L., Zhang, Y., Yuan, S., Su, Q., Sun, S., Wu, C., Yao, W., Han, T., & Hou, W. (2020) · Plant Biotechnology Journal · doi:10.1111/pbi.13386 · Cited by 112 · see citing works

Efficient precise in vivo base editing in adult dystrophic mice

Xu, L. M., Zhang, C., Bailin, P. L., Wang, P., Gao, Y., Mohler, P. J., Mokadam, N. A., Ma, J., Arnold, W. D., & Han, R. (2021) · Nature Communications · doi:10.1038/s41467-021-23996-y · Cited by 109 · see citing works

CRISPR-Based Gene Therapies: From Preclinical to Clinical Treatments

Laurent, M., Geoffroy, M., Pavani, G., & Guiraud, S. (2024) · Cells · doi:10.3390/cells13100800 · Cited by 122 · see citing works

Tools for experimental and computational analyses of off-target editing by programmable nucleases

Bao, X. R., Pan, Y., Lee, C. M., Davis, T. H., & Bao, G. (2021) · Nature Protocols · doi:10.1038/s41596-020-00431-y · Cited by 106 · see citing works

CRISPR/Cas brings plant biology and breeding into the fast lane

Schindele, A., Dorn, A., & Puchta, H. (2019) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2019.08.006 · Cited by 110 · see citing works

Precise base editing of non-allelic acetolactate synthase genes confers sulfonylurea herbicide resistance in maize

Li, Y., Zhu, J., Wu, H., Liu, C., Huang, C., Lan, J., Zhao, Y., & Xie, C. (2019) · The Crop Journal · doi:10.1016/j.cj.2019.10.001 · Cited by 112 · see citing works

Structure-based functional mechanisms and biotechnology applications of anti-CRISPR proteins

Jia, N., & Patel, D. J. (2021) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-021-00371-9 · Cited by 108 · see citing works

Allogeneic CAR-T Therapy Technologies: Has the Promise Been Met?

Lonez, C., & Breman, E. (2024) · Cells · doi:10.3390/cells13020146 · Cited by 113 · see citing works

CRISPR technologies for stem cell engineering and regenerative medicine

Hsu, M., Chang, Y., Truong, V. A., Lai, P., Nguyen, T. K. N., & Hu, Y. (2019) · Biotechnology Advances · doi:10.1016/j.biotechadv.2019.107447 · Cited by 105 · see citing works

Eliminating base-editor-induced genome-wide and transcriptome-wide off-target mutations

Wang, L., Xue, W., Zhang, H., Gao, R., Qiu, H.-Y., Wei, J., Zhou, L., Lei, Y.-N., Wu, X., Li, X., et al. (2021) · Nature Cell Biology · doi:10.1038/s41556-021-00671-4 · Cited by 103 · see citing works

CRISPR engineering in organoids for gene repair and disease modelling

Geurts, M. H., & Clevers, H. (2023) · Nature Reviews Bioengineering · doi:10.1038/s44222-022-00013-5 · Cited by 103 · see citing works

Generating broad-spectrum tolerance to ALS-inhibiting herbicides in rice by base editing

Zhang, R., Chen, S., Meng, X., Chai, Z., Wang, D., Yuan, Y., Chen, K., Jiang, L., Li, J., & Gao, C. (2020) · Science China Life Sciences · doi:10.1007/s11427-020-1800-5 · Cited by 101 · see citing works

A Highly Efficient CRISPR-Cas9-Based Genome Engineering Platform in Acinetobacter baumannii to Understand the H2O2-Sensing Mechanism of OxyR

Wang, Y., Wang, Z., Chen, Y., Hua, X., Yu, Y., & Ji, Q. (2019) · Cell chemical biology · doi:10.1016/j.chembiol.2019.09.003 · Cited by 93 · see citing works

Green Revolution to Gene Revolution: Technological Advances in Agriculture to Feed the World

Hamdan, M. F., Noor, S. N. M., Abd-Aziz, N., Pua, T., & Tan, B. C. (2022) · Plants · doi:10.3390/plants11101297 · Cited by 101 · see citing works

Advances in Genome Editing With CRISPR Systems and Transformation Technologies for Plant DNA Manipulation

Nadakuduti, S. S., & Enciso-Rodríguez, F. E. (2021) · Frontiers in Plant Science · doi:10.3389/fpls.2020.637159 · Cited by 98 · see citing works

Reverse-genetics studies of lncRNAs—what we have learnt and paths forward

Gao, F., Cai, Y., Kapranov, P., & Xu, D. (2020) · Genome biology · doi:10.1186/s13059-020-01994-5 · Cited by 92 · see citing works

High-purity production and precise editing of DNA base editing ribonucleoproteins

Jang, H.-K., Jo, D. H., Lee, S.-N., Cho, C. S., Jeong, Y. K., Jung, Y., Yu, J., Kim, J. H., Woo, J.-S., & Bae, S. (2021) · Science Advances · doi:10.1126/sciadv.abg2661 · Cited by 93 · see citing works

Off-Target Editing by CRISPR-Guided DNA Base Editors

Park, S., & Beal, P. A. (2019) · Biochemistry · doi:10.1021/acs.biochem.9b00573 · Cited by 92 · see citing works

CRISPR/Cas genome editing improves abiotic and biotic stress tolerance of crops

Li, Y., Wu, X., Zhang, Y., & Zhang, Q. (2022) · Frontiers in Genome Editing · doi:10.3389/fgeed.2022.987817 · Cited by 96 · see citing works

Plant base editing and prime editing: The current status and future perspectives

Li, J., Zhang, C., He, Y., Li, S., Yan, L., Li, Y., Zhu, Z., & Xia, L. (2022) · Journal of Integrative Plant Biology · doi:10.1111/jipb.13425 · Cited by 93 · see citing works

Advancing protein evolution with inverse folding models integrating structural and evolutionary constraints

Fei, H., Li, Y., Liu, Y., Wei, J., Chen, A. A., & Gao, C. (2025) · Cell · doi:10.1016/j.cell.2025.06.014 · Cited by 92 · see citing works

Development and Application of Base Editors

Yang, B., Yang, L. C., & Chen, J. (2019) · The CRISPR Journal · doi:10.1089/crispr.2019.0001 · Cited by 86 · see citing works

Glycosylase-based base editors for efficient T-to-G and C-to-G editing in mammalian cells

Ye, L., Zhao, D., Li, J., Wang, Y., Li, B., Yang, Y., Hou, X., Wang, H., Wei, Z., Liu, X., et al. (2024) · Nature Biotechnology · doi:10.1038/s41587-023-02050-w · Cited by 88 · see citing works

Base editing with high efficiency in allotetraploid oilseed rape by A3A‐PBE system

Cheng, H., Hao, M., Ding, B., Mei, D., Wang, W., Wang, H., Zhou, R., Liu, J., Li, C., & Hu, Q. (2020) · Plant Biotechnology Journal · doi:10.1111/pbi.13444 · Cited by 83 · see citing works

Rationally Designed Base Editors for Precise Editing of the Sickle Cell Disease Mutation

Chu, S. H., Packer, M. S., Rees, H. A., Lam, D. K., Yu, Y., Marshall, J., Cheng, L.-I., Lam, D., Olins, J., Ran, F. A., et al. (2021) · The CRISPR Journal · doi:10.1089/crispr.2020.0144 · Cited by 79 · see citing works

Cytosine base editor generates substantial off-target single-nucleotide variants in mouse embryos

Zuo, E., Sun, Y., Wei, W., Yuan, T., Ying, W., Sun, H., Yuan, L., Steinmetz, L. M., Li, Y., & Yang, H. (2019) · Science · doi:10.1126/science.aav9973 · Cited by 782 · see citing works

Cytosine base editors go off-target

Wrighton, K. H. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-019-0110-x · Cited by 3 · see citing works

Spotting off-targets from gene editing

Mao, S. (2019) · Science · doi:10.1126/science.364.6437.249-b

Expanding the base editing scope in rice by using Cas9 variants

Hua, K., Tao, X., & Zhu, J. (2018) · Plant Biotechnology Journal · doi:10.1111/pbi.12993 · Cited by 214 · see citing works

Response to “Unexpected mutations after CRISPR–Cas9 editing in vivo”

Lareau, C. A., Clement, K., Hsu, J. Y., Pattanayak, V., Joung, J. K., Aryee, M. J., & Pinello, L. (2018) · Nature Methods · doi:10.1038/nmeth.4541 · Cited by 32 · see citing works