The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.
Target prediction for small, noncoding RNAs in bacteria
Open accessAbstract
Many small, noncoding RNAs in bacteria act as post-transcriptional regulators by basepairing with target mRNAs. While the number of characterized small RNAs (sRNAs) has steadily increased, only a limited number of the corresponding mRNA targets have been identified. Here we present a program, TargetRNA, that predicts the targets of these bacterial RNA regulators. The program was evaluated by assessing whether previously known targets could be identified. The program was then used to predict targets for the Escherichia coli RNAs RyhB, OmrA, OmrB and OxyS, and the predictions were compared with changes in whole genome expression patterns observed upon expression of the sRNAs. Our results show that TargetRNA is a useful tool for finding mRNA targets of sRNAs, although its rate of success varies between sRNAs.
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Cites
Mfold web server for nucleic acid folding and hybridization prediction
Zuker, M. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg595 · Cited by 13,404
Prediction of Mammalian MicroRNA Targets
Lewis, B. P., Shih, I.-H., Jones-Rhoades, M. W., Bartel, D. P., & Burge, C. B. (2003) · Cell · doi:10.1016/s0092-8674(03)01018-3 · Cited by 5,199
Combinatorial microRNA target predictions
Krek, A., Grün, D., Poy, M. N., Wolf, R., Rosenberg, L., Epstein, E. J., MacMenamin, P., da Piedade, I., Gunsalus, K. C., Stoffel, M., et al. (2005) · Nature Genetics · doi:10.1038/ng1536 · Cited by 4,603
Mathews, D. H., Sabina, J., Zuker, M., & Turner, D. H. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1999.2700 · Cited by 3,795
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Cited by
TonB-dependent transporters: regulation, structure, and function
Noinaj, N., Guillier, M., Barnard, & Buchanan, S. K. (2010) · Annual Review of Microbiology · doi:10.1146/annurev.micro.112408.134247 · Cited by 989
Self-citationBusch, A., Richter, A. S., & Backofen, R. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn544 · Cited by 552
Small RNA Binding to 5′ mRNA Coding Region Inhibits Translational Initiation
Bouvier, M., Sharma, C. M., Mika, F., Nierhaus, K. H., & Vogel, J. (2008) · Molecular Cell · doi:10.1016/j.molcel.2008.10.027 · Cited by 270
Gaballa, A., Antelmann, H., Aguilar, C., Khakh, S. K., Song, K.-B., Smaldone, G. T., & Helmann, J. D. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0711752105 · Cited by 232
Deep sequencing-based identification of small non-coding RNAs in Streptomyces coelicolor
Vockenhuber, M.-P., Sharma, C. M., Statt, M. G., Schmidt, D., Xu, Z., Dietrich, S., Liesegang, H., Mathews, D. H., & Suess, B. (2011) · RNA Biology · doi:10.4161/rna.8.3.14421 · Cited by 88
Metadata
- Authors
- Tjaden, B., Goodwin, S. S., Opdyke, J. A., Guillier, M., Fu, D. X., Gottesman, S., & Storz, G.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2006-05-22
- Volume
- 34
- Issue
- 9
- Pages
- 2791-2802
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2139271133
- Cited by
- 252
- References
- 5
- FWCI
- 10.43
- Type
- journal article
- Language
- en
- Open access
- gold
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- Tjaden, B., Goodwin, S. S., Opdyke, J. A., Guillier, M., Fu, D. X., Gottesman, S., & Storz, G. (2006). Target prediction for small, noncoding RNAs in bacteria. Nucleic Acids Research. https://doi.org/10.1093/nar/gkl356
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