The DOI matches its Crossref record; 32 of the 32 references it cites were found in a registry or an index.
CHOPCHOP v3: expanding the CRISPR web toolbox beyond genome editing
Open accessAbstract
The CRISPR–Cas system is a powerful genome editing tool that functions in a diverse array of organisms and cell types. The technology was initially developed to induce targeted mutations in DNA, but CRISPR–Cas has now been adapted to target nucleic acids for a range of purposes. CHOPCHOP is a web tool for identifying CRISPR–Cas single guide RNA (sgRNA) targets. In this major update of CHOPCHOP, we expand our toolbox beyond knockouts. We introduce functionality for targeting RNA with Cas13, which includes support for alternative transcript isoforms and RNA accessibility predictions. We incorporate new DNA targeting modes, including CRISPR activation/repression, targeted enrichment of loci for long-read sequencing, and prediction of Cas9 repair outcomes. Finally, we expand our results page visualization to reveal alternative isoforms and downstream ATG sites, which will aid users in avoiding the expression of truncated proteins. The CHOPCHOP web tool now supports over 200 genomes and we have released a command-line script for running larger jobs and handling unsupported genomes. CHOPCHOP v3 can be found at https://chopchop.cbu.uib.no
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Cites
Multiplex Genome Engineering Using CRISPR/Cas Systems
Cong, L., Ran, F. A., Cox, D., Lin, S., Barretto, R., Habib, N., Hsu, P. D., Wu, X., Jiang, W., Marraffini, L. A., et al. (2013) · Science · doi:10.1126/science.1231143 · Cited by 15,339
Lorenz, R., Bernhart, S. H., Höner zu Siederdissen, C., Tafer, H., Flamm, C., Stadler, P. F., & Hofacker, I. L. (2011) · Algorithms for Molecular Biology · doi:10.1186/1748-7188-6-26 · Cited by 5,098
Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression
Qi, L. S., Larson, M. H., Gilbert, L. A., Doudna, J. A., Weissman, J. S., Arkin, A. P., & Lim, W. A. (2013) · Cell · doi:10.1016/j.cell.2013.02.022 · Cited by 5,016
DNA targeting specificity of RNA-guided Cas9 nucleases
Hsu, P. D., Scott, D. A., Weinstein, J. A., Ran, F. A., Konermann, S., Agarwala, V., Li, Y., Fine, E. J., Wu, X., Shalem, O., et al. (2013) · Nature Biotechnology · doi:10.1038/nbt.2647 · Cited by 4,741
Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9
Doench, J. G., Fusi, N., Sullender, M., Hegde, M., Vaimberg, E. W., Donovan, K. F., Smith, I., Tothova, Z., Wilen, C., Orchard, R., et al. (2016) · Nature Biotechnology · doi:10.1038/nbt.3437 · Cited by 4,637
Nucleic acid detection with CRISPR-Cas13a/C2c2
Gootenberg, J. S., Abudayyeh, O. O., Lee, J. W., Essletzbichler, P., Dy, A. J., Joung, J., Verdine, V., Donghia, N., Daringer, N. M., Freije, C. A., et al. (2017) · Science · doi:10.1126/science.aam9321 · Cited by 3,844
CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes
Gilbert, L. A., Larson, M. H., Morsut, L., Liu, Z., Brar, G. A., Torres, S. E., Stern-Ginossar, N., Brandman, O., Whitehead, E. H., Doudna, J. A., et al. (2013) · Cell · doi:10.1016/j.cell.2013.06.044 · Cited by 3,696 · cited 1×
“For instance, CRISPR–Cas has been used to introduce new sequences into the genome (1–3), activate (4,5) or repress (6) transcription, as an enrichment tool for sequencing (7,8), for targeted hypermutation (9), as a diagnostic tool (10), to perform whole-organism lineage tracing (11), to target RNA molecules for destru…”
MethodC2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector
Abudayyeh, O. O., Gootenberg, J. S., Konermann, S., Joung, J., Slaymaker, I. M., Cox, D. B. T., Shmakov, S., Makarova, K. S., Semenova, E., Minakhin, L., et al. (2016) · Science · doi:10.1126/science.aaf5573 · Cited by 2,336
RNA targeting with CRISPR–Cas13
Abudayyeh, O. O., Gootenberg, J. S., Essletzbichler, P., Han, S., Joung, J., Belanto, J. J., Verdine, V., Cox, D. B. T., Kellner, M. J., Regev, A., et al. (2017) · Nature · doi:10.1038/nature24049 · Cited by 2,093
Cox, D. B. T., Gootenberg, J. S., Abudayyeh, O. O., Franklin, B., Kellner, M. J., Joung, J., & Zhang, F. (2017) · Science · doi:10.1126/science.aaq0180 · Cited by 1,834
Cited by
Inhibition of PCSK9 potentiates immune checkpoint therapy for cancer
Liu, X., Bao, X., Hu, M., Chang, H., Jiao, M., Cheng, J., Xie, L., Huang, Q., Li, F., & Li, C.-Y. (2020) · Nature · doi:10.1038/s41586-020-2911-7 · Cited by 490
First report of CRISPR/cas9 mediated dna-free editing of 4cl and rve7 genes in chickpea protoplasts
Badhan, S., Ball, A. S., & Mantri, N. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22010396 · Cited by 193
Dual-AAV delivering split prime editor system for in vivo genome editing
Zhi, S., Chen, Y., Wu, G., Wen, J., Wu, J., Liu, Q., Li, Y., Kang, R., Hu, S., Wang, J., et al. (2022) · Molecular Therapy · doi:10.1016/j.ymthe.2021.07.011 · Cited by 174
Saturation variant interpretation using CRISPR prime editing
Erwood, S., Bily, T. M. I., Lequyer, J., Yan, J., Gulati, N., Brewer, R. A., Zhou, L., Pelletier, L., Ivakine, E. A., & Cohn, R. D. (2022) · Nature Biotechnology · doi:10.1038/s41587-021-01201-1 · Cited by 163
Plebanek, M. P., Xue, Y., Nguyen, Y.-V., DeVito, N. C., Wang, X., Holtzhausen, A., Beasley, G. M., Theivanthiran, B., & Hanks, B. A. (2024) · Science Immunology · doi:10.1126/sciimmunol.adi4191 · Cited by 164
Metadata
- Authors
- Labun, K., Montague, T. G., Krause, M., Torres Cleuren, Y. N., Tjeldnes, H., & Valen, E.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2019-05-20
- Volume
- 47
- Issue
- W1
- Pages
- W171-W174
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2945567049
- Cited by
- 2,054
- References
- 32
- FWCI
- 46.12
- Type
- journal article
- Language
- en
- Open access
- gold
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- Labun, K., Montague, T. G., Krause, M., Torres Cleuren, Y. N., Tjeldnes, H., & Valen, E. (2019). CHOPCHOP v3: expanding the CRISPR web toolbox beyond genome editing. Nucleic Acids Research. https://doi.org/10.1093/nar/gkz365
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