The DOI matches its Crossref record; 28 of the 28 references it cites were found in a registry or an index.
TAL Effector-Nucleotide Targeter (TALE-NT) 2.0: tools for TAL effector design and target prediction
Open accessAbstract
Transcription activator-like (TAL) effectors are repeat-containing proteins used by plant pathogenic bacteria to manipulate host gene expression. Repeats are polymorphic and individually specify single nucleotides in the DNA target, with some degeneracy. A TAL effector-nucleotide binding code that links repeat type to specified nucleotide enables prediction of genomic binding sites for TAL effectors and customization of TAL effectors for use in DNA targeting, in particular as custom transcription factors for engineered gene regulation and as site-specific nucleases for genome editing. We have developed a suite of web-based tools called TAL Effector-Nucleotide Targeter 2.0 (TALE-NT 2.0; https://boglab.plp.iastate.edu/) that enables design of custom TAL effector repeat arrays for desired targets and prediction of TAL effector binding sites, ranked by likelihood, in a genome, promoterome or other sequence of interest. Search parameters can be set by the user to work with any TAL effector or TAL effector nuclease architecture. Applications range from designing highly specific DNA targeting tools and identifying potential off-target sites to predicting effector targets important in plant disease.
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Cites
Biopython: freely available python tools for computational molecular biology and bioinformatics
Cock, P. J. A., Antao, T., Chang, J. T., Chapman, B. A., Cox, C. J., Dalke, A., Friedberg, I., Hamelryck, T., Kauff, F., Wilczynski, B., et al. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp163 · Cited by 6,080
Breaking the Code of DNA Binding Specificity of TAL-Type III Effectors
Boch, J., Scholze, H., Schornack, S., Landgraf, A., Hahn, S., Kay, S., Lahaye, T., Nickstadt, A., & Bonas, U. (2009) · Science · doi:10.1126/science.1178811 · Cited by 2,470
A TALE nuclease architecture for efficient genome editing
Miller, J. C., Tan, S., Qiao, G., Barlow, K. A., Wang, J., Xia, D. F., Meng, X., Paschon, D. E., Leung, E., Hinkley, S. J., et al. (2011) · Nature Biotechnology · doi:10.1038/nbt.1755 · Cited by 2,098
A Simple Cipher Governs DNA Recognition by TAL Effectors
Moscou, M. J., & Bogdanove, A. J. (2009) · Science · doi:10.1126/science.1178817 · Cited by 1,988
Self-citationTargeting DNA Double-Strand Breaks with TAL Effector Nucleases
Christian, M., Cermak, T., Doyle, E. L., Schmidt, C., Zhang, F., Hummel, A., Bogdanove, A. J., & Voytas, D. F. (2010) · Genetics · doi:10.1534/genetics.110.120717 · Cited by 1,869
Self-citationCermak, T., Doyle, E. L., Christian, M., Wang, L., Zhang, Y., Schmidt, C., Baller, J. A., Somia, N. V., Bogdanove, A. J., & Voytas, D. F. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr218 · Cited by 1,787
Self-citationGenetic engineering of human pluripotent cells using TALE nucleases
Hockemeyer, D., Wang, H., Kiani, S., Lai, C. S., Gao, Q., Cassady, J. P., Cost, G. J., Zhang, L., Santiago, Y., Miller, J. C., et al. (2011) · Nature Biotechnology · doi:10.1038/nbt.1927 · Cited by 1,135
FLASH assembly of TALENs for high-throughput genome editing
Reyon, D., Tsai, S. Q., Khayter, C., Foden, J. A., Sander, J. D., & Joung, J. K. (2012) · Nature Biotechnology · doi:10.1038/nbt.2170 · Cited by 1,093
TAL effectors: customizable proteins for DNA targeting
Bogdanove, A. J., & Voytas, D. F. (2011) · Science · doi:10.1126/science.1204094 · Cited by 984
Self-citationA novel TALE nuclease scaffold enables high genome editing activity in combination with low toxicity
Mussolino, C., Morbitzer, R., Lütge, F., Dannemann, N., Lahaye, T., & Cathomen, T. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr597 · Cited by 714
Cited by
TALENs: A widely applicable technology for targeted genome editing
Joung, J. K., & Sander, J. D. (2013) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3486 · Cited by 1,650
“In addition, it has been suggested that users should apply computationally derived design guidelines (originally proposed for dimeric TALENs 15 ) to monomeric TALE-based transcription factors 100 but no published experimental support yet exists for this recommendation.”
A CRISPR/Cas9 Toolbox for Multiplexed Plant Genome Editing and Transcriptional Regulation
Lowder, L. G., Zhang, D., Baltes, N. J., Paul, J. W., Tang, X., Zheng, X., Voytas, D. F., Hsieh, T.-F., Zhang, Y., & Qi, Y. (2015) · Plant Physiology · doi:10.1104/pp.15.00636 · Cited by 707
Self-citationGenome-wide detection of DNA double-stranded breaks induced by engineered nucleases
Frock, R. L., Hu, J., Meyers, R. M., Ho, Y.-J., Kii, E., & Alt, F. W. (2015) · Nature Biotechnology · doi:10.1038/nbt.3101 · Cited by 673
Targeted Mutagenesis in Zea mays Using TALENs and the CRISPR/Cas System
Liang, Z., Zhang, K., Chen, K., & Gao, C. (2014) · Journal of Genetics and Genomics · doi:10.1016/j.jgg.2013.12.001 · Cited by 658
Poirot, L., Philip, B., Schiffer-Mannioui, C., Le Clerre, D., Chion-Sotinel, I., Derniame, S., Potrel, P., Bas, C., Lemaire, L., Galetto, R., et al. (2015) · Cancer Research · doi:10.1158/0008-5472.can-14-3321 · Cited by 605
Metadata
- Authors
- Doyle, E. L., Booher, N. J., Standage, D. S., Voytas, D. F., Brendel, V. P., VanDyk, J. K., & Bogdanove, A. J.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2012-06-12
- Volume
- 40
- Issue
- W1
- Pages
- W117-W122
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2114838239
- Cited by
- 586
- References
- 28
- FWCI
- 27.18
- Type
- journal article
- Language
- en
- Open access
- gold
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- Doyle, E. L., Booher, N. J., Standage, D. S., Voytas, D. F., Brendel, V. P., VanDyk, J. K., & Bogdanove, A. J. (2012). TAL Effector-Nucleotide Targeter (TALE-NT) 2.0: tools for TAL effector design and target prediction. Nucleic Acids Research. https://doi.org/10.1093/nar/gks608
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