Rationally designed APOBEC3B cytosine base editors with improved specificity

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

WebLogo: A Sequence Logo Generator: Figure 1Preprint

Crooks, G. E., Hon, G. C., Chandonia, J., & Brenner, S. E. (2004) · Genome Research · doi:10.1101/gr.849004 · Cited by 12,433 · 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

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

Walker, B. J., Abeel, T., Shea, T., Priest, M., Abouelliel, A., Sakthikumar, S., Cuomo, C. A., Zeng, Q., Wortman, J. R., Young, S., et al. (2014) · PLoS ONE · doi:10.1371/journal.pone.0112963 · Cited by 8,994 · see citing works

Canu: scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separationPreprint

Koren, S., Walenz, B. P., Berlin, K., Miller, J. R., Bergman, N. H., & Phillippy, A. M. (2017) · Genome Research · doi:10.1101/gr.215087.116 · Cited by 7,340 · 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

BUSCO applications from quality assessments to gene prediction and phylogenomics

Waterhouse, R. M., Seppey, M., Simão, F. A., Manni, M., Ioannidis, P., Klioutchnikov, G., Kriventseva, E. V., & Zdobnov, E. M. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msx319 · Cited by 2,214 · 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

CRISPR/Cas Genome Editing and Precision Plant Breeding in Agriculture

Chen, K., Wang, Y., Zhang, R., Zhang, H., & Gao, C. (2019) · Annual Review of Plant Biology · doi:10.1146/annurev-arplant-050718-100049 · 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

Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies

Roach, M. J., Schmidt, S. A., & Borneman, A. R. (2018) · BMC Bioinformatics · doi:10.1186/s12859-018-2485-7 · Cited by 1,152 · see citing works

CRISPR-Based Technologies for the Manipulation of Eukaryotic Genomes

Komor, A. C., Badran, A. H., & Liu, D. R. (2016) · Cell · doi:10.1016/j.cell.2016.10.044 · Cited by 1,011 · 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

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

Jin, S., Zong, Y., Gao, Q., Zhu, Z., Wang, Y., Qin, P., Liang, C., Wang, D., Qiu, J.-L., Zhang, F., et al. (2019) · Science · doi:10.1126/science.aaw7166 · Cited by 665 · see citing works

Transcriptome-wide off-target RNA editing induced by CRISPR-guided DNA base editors

Grünewald, J., Zhou, R., Garcia, S. P., Iyer, S., Lareau, C. A., Aryee, M. J., & Joung, J. K. (2019) · Nature · doi:10.1038/s41586-019-1161-z · Cited by 663 · 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

Adenine base editing in mouse embryos and an adult mouse model of Duchenne muscular dystrophy

Ryu, S.-M., Koo, T., Kim, K., Lim, K., Baek, G., Kim, S., Kim, H. S., Kim, D.-E., Lee, H., Chung, E., et al. (2018) · Nature Biotechnology · doi:10.1038/nbt.4148 · Cited by 442 · 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

Efficient C-to-T base editing in plants using a fusion of nCas9 and human APOBEC3A

Zong, Y., Song, Q., Li, C., Jin, S., Zhang, D., Wang, Y., Qiu, J., & Gao, C. (2018) · Nature Biotechnology · doi:10.1038/nbt.4261 · Cited by 433 · 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

ALLMAPS: robust scaffold ordering based on multiple maps

Tang, H.-B., Zhang, X.-T., Miao, C., Zhang, J.-S., Ming, R., Schnable, J., Schnable, P., Lyons, E., & Lu, J.-G. (2015) · Genome Biology · doi:10.1186/s13059-014-0573-1 · Cited by 376 · see citing works

Generation of herbicide tolerance traits and a new selectable marker in wheat using base editing

Zhang, R., Liu, J., Chai, Z., Chen, S., Bai, Y., Zong, Y., Chen, K., Li, J., Jiang, L., & Gao, C. (2019) · Nature Plants · doi:10.1038/s41477-019-0405-0 · Cited by 340 · see citing works

CRISPR DNA base editors with reduced RNA off-target and self-editing activities

Grünewald, J., Zhou, R., Iyer, S., Lareau, C. A., Garcia, S. P., Aryee, M. J., & Joung, J. K. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0236-6 · Cited by 332 · see citing works

A large-scale whole-genome sequencing analysis reveals highly specific genome editing by both Cas9 and Cpf1 (Cas12a) nucleases in rice

Tang, X. D., Liu, G., Zhou, J., Ren, Q., You, Q., Tian, L., Xin, X., Zhong, Z., Liu, B., Zheng, X., et al. (2018) · Genome biology · doi:10.1186/s13059-018-1458-5 · Cited by 305 · 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

Efficient base editing in methylated regions with a human APOBEC3A-Cas9 fusion

Wang, X., Li, J., Wang, Y., Yang, B., Wei, J., Wu, J., Wang, R., Huang, X., Chen, J., & Yang, L. C. (2018) · Nature Biotechnology · doi:10.1038/nbt.4198 · Cited by 264 · see citing works

In Vivo Base Editing of PCSK9 (Proprotein Convertase Subtilisin/Kexin Type 9) as a Therapeutic Alternative to Genome Editing

Chadwick, A. C., Wang, X., & Musunuru, K. (2017) · Arteriosclerosis Thrombosis and Vascular Biology · doi:10.1161/atvbaha.117.309881 · Cited by 218 · see citing works

Correction of β-thalassemia mutant by base editor in human embryos

Liang, P., Ding, C., Sun, H., Xie, X., Xu, Y., Zhang, X., Sun, Y., Xiong, Y., Ma, W., Liu, Y., et al. (2017) · Protein & Cell · doi:10.1007/s13238-017-0475-6 · Cited by 217 · see citing works

Whole genome sequencing reveals rare off‐target mutations and considerable inherent genetic or/and somaclonal variations in CRISPR /Cas9‐edited cotton plants

Li, J., Manghwar, H., Sun, L., Wang, P., Wang, G., Sheng, H., Zhang, J., Liu, H., Qin, L., Rui, H., et al. (2018) · Plant Biotechnology Journal · doi:10.1111/pbi.13020 · Cited by 205 · see citing works

No unexpected CRISPR-Cas9 off-target activity revealed by trio sequencing of gene-edited mice

Iyer, V., Boroviak, K., Thomas, M., Doe, B., Riva, L., Ryder, E., & Adams, D. J. (2018) · PLoS Genetics · doi:10.1371/journal.pgen.1007503 · Cited by 123 · see citing works

Crystal Structure of the DNA Deaminase APOBEC3B Catalytic Domain

Shi, K., Carpenter, M. A., Kurahashi, K., Harris, R. S., & Aihara, H. (2015) · Journal of Biological Chemistry · doi:10.1074/jbc.m115.679951 · Cited by 98 · 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

A fluorescent reporter for quantification and enrichment of DNA editing by APOBEC–Cas9 or cleavage by Cas9 in living cells

Martin, A. S., Salamango, D. J., Serebrenik, A. A., Shaban, N. M., Brown, W. L., Donati, F., Munagala, U., Conticello, S. G., & Harris, R. S. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky332 · Cited by 81 · see citing works

Expanding the genome-targeting scope and the site selectivity of high-precision base editors

Tan, J., Zhang, F., Karcher, D., & Bock, R. (2020) · Nature Communications · doi:10.1038/s41467-020-14465-z · Cited by 78 · see citing works

Expanding C–T base editing toolkit with diversified cytidine deaminases

Cheng, T., Li, S., Yuan, B., Wang, X., Zhou, W., & Qiu, Z. (2019) · Nature Communications · doi:10.1038/s41467-019-11562-6 · Cited by 72 · see citing works

Manipulating mRNA splicing by base editing in plants

Xue, C., Zhang, H., Lin, Q., Fan, R., & Gao, C. (2018) · Science China Life Sciences · doi:10.1007/s11427-018-9392-7 · Cited by 65 · see citing works

Targeting specificity of APOBEC-based cytosine base editor in human iPSCs determined by whole genome sequencing

McGrath, E. L., Shin, H., Zhang, L., Phue, J., Wu, W. W., Shen, R., Jang, Y.-Y., Revollo, J. R., & Ye, Z. (2019) · Nature Communications · doi:10.1038/s41467-019-13342-8 · Cited by 63 · see citing works

Nuclear Magnetic Resonance Structure of the APOBEC3B Catalytic Domain: Structural Basis for Substrate Binding and DNA Deaminase Activity

Byeon, I. L., Byeon, C., Wu, T., Mitra, M., Singer, D., Levin, J. G., & Gronenborn, A. M. (2016) · Biochemistry · doi:10.1021/acs.biochem.6b00382 · Cited by 61 · see citing works

Cytosine base editor 4 but not adenine base editor generates off-target mutations in mouse embryos

Lee, H., Smith, H. E., Liu, C., Willi, M., & Hennighausen, L. G. (2020) · Communications Biology · doi:10.1038/s42003-019-0745-3 · Cited by 57 · see citing works

Mutation frequency is not increased in CRISPR–Cas9-edited mice

Willi, M., Smith, H. E., Wang, C., et al. (2018) · Nature Methods · doi:10.1038/s41592-018-0148-2 · Cited by 36 · see citing works

Characterization of the Catalytic Domain of Human APOBEC3B and the Critical Structural Role for a Conserved Methionine

Siriwardena, S. U., Guruge, T. A., & Bhagwat, A. S. (2015) · Journal of Molecular Biology · doi:10.1016/j.jmb.2015.08.006 · Cited by 33 · see citing works

BIGpre: A Quality Assessment Package for Next-Generation Sequencing Data

Zhang, T., Luo, Y., Liu, K., Pan, L., Zhang, B., Yu, J. M., & Hu, S. (2011) · Genomics Proteomics & Bioinformatics · doi:10.1016/s1672-0229(11)60027-2 · Cited by 33 · see citing works

Structural Analysis of the Active Site and DNA Binding of Human Cytidine Deaminase APOBEC3B

Hou, S., Silvas, T. V., Leidner, F., et al. (2018) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.8b00545 · Cited by 25 · see citing works

Generation of Stable Transgenic Rice (Oryza sativa L.) by Agrobacterium‐Mediated Transformation

Zhang, Y., Li, J., & Gao, C. (2016) · Current Protocols in Plant Biology · doi:10.1002/cppb.20004 · Cited by 20 · see citing works

Applications of CRISPR–Cas in agriculture and plant biotechnology

Zhu, H., Li, C., & Gao, C. (2020) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-020-00288-9 · Cited by 870 · 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

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

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

Genome-wide analyses of PAM-relaxed Cas9 genome editors reveal substantial off-target effects by ABE8e in rice

Wu, Y., Ren, Q., Zhong, Z., Liu, G., Han, Y., Bao, Y., Liu, L., Xiang, S., Liu, S., Tang, X., et al. (2022) · Plant Biotechnology Journal · doi:10.1111/pbi.13838 · Cited by 56 · see citing works

Putting CRISPR-Cas system in action: a golden window for efficient and precise genome editing for crop improvement

Tariq, A., Mushtaq, M., Yaqoob, H., Bhat, B. A., Zargar, S. M., Raza, A., Ali, S., Charagh, S., Mubarik, M. S., Zaman, Q. U., et al. (2023) · GM Crops & Food · doi:10.1080/21645698.2023.2219111 · Cited by 45 · see citing works

A cytosine base editor toolkit with varying activity windows and target scopes for versatile gene manipulation in plants

Xiong, X., Li, Z., Liang, J., Liu, K., Li, C., & Li, J.-F. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac166 · Cited by 41 · see citing works

Cytidine Deaminase Inhibitor

National Cancer Institute (2020) · Definitions · doi:10.32388/uzrcrb

A survey of cytosine and cytidine salvage in fungi

Kulkarni, R. K., Krzycki, J. A., & Nickerson, K. W. (1980) · Experimental Mycology · doi:10.1016/0147-5975(80)90014-6 · Cited by 3 · see citing works

An Enzymatic Assay for High-Throughput Screening of Cytidine-Producing Microbial Strains

Dong, H., Liu, Y., Zu, X. L., et al. (2015) · PLoS ONE · doi:10.1371/journal.pone.0121612 · Cited by 20 · see citing works

Regulation of Pyrimidine Nucleotide Biosynthesis in Cytidine Deaminase-negative Mutants of Bacillus subtilis

Asahi, S., Doi, M., Tsunemi, Y., et al. (1989) · Agricultural and Biological Chemistry · doi:10.1080/00021369.1989.10869269 · Cited by 11 · see citing works

2,2'-O-cyclocytidine, an antitumor cytidine analog resistant to cytidine deaminase.

Hoshi, A., Kanazawa, F., Kuretani, K., et al. (1971) · PubMed · Cited by 23 · see citing works