The DOI matches its Crossref record; 21 of the 21 references it cites were found in a registry or an index.
siDirect: highly effective, target-specific siRNA design software for mammalian RNA interference
Open accessAbstract
siDirect (http://design.RNAi.jp/) is a web-based online software system for computing highly effective small interfering RNA (siRNA) sequences with maximum target-specificity for mammalian RNA interference (RNAi). Highly effective siRNA sequences are selected using novel guidelines that were established through an extensive study of the relationship between siRNA sequences and RNAi activity. Our efficient software avoids off-target gene silencing to enumerate potential cross-hybridization candidates that the widely used BLAST search may overlook. The website accepts an arbitrary sequence as input and quickly returns siRNA candidates, providing a wide scope of applications in mammalian RNAi, including systematic functional genomics and therapeutic gene silencing.
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Cites
Basic local alignment search tool
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Identification of common molecular subsequences
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Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells
Elbashir, S. M., Harborth, J., Lendeckel, W., Yalcin, A., Weber, K., & Tuschl, T. (2001) · Nature · doi:10.1038/35078107 · Cited by 9,456
Hannon, G. J. (2002) · Nature · doi:10.1038/418244a · Cited by 3,538
RNA interference is mediated by 21- and 22-nucleotide RNAs
Elbashir, S. M., Lendeckel, W., & Tuschl, T. (2001) · Genes & Development · doi:10.1101/gad.862301 · Cited by 3,310
Asymmetry in the Assembly of the RNAi Enzyme Complex
Schwarz, D. S., Hutvágner, G., Du, T., Xu, Z., Aronin, N., & Zamore, P. D. (2003) · Cell · doi:10.1016/s0092-8674(03)00759-1 · Cited by 2,922
Functional siRNAs and miRNAs exhibit strand bias
Khvorova, A., Reynolds, A., & Jayasena, S. D. (2003) · Cell · doi:10.1016/s0092-8674(03)00801-8 · Cited by 2,645
Expression profiling reveals off-target gene regulation by RNAi
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Single-Stranded Antisense siRNAs Guide Target RNA Cleavage in RNAi
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Killing the messenger: short RNAs that silence gene expression
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Cited by
CircInteractome: A web tool for exploring circular RNAs and their interacting proteins and microRNAs
Dudekula, D. B., Panda, A. C., Grammatikakis, I., De, S., Abdelmohsen, K., & Gorospe, M. (2016) · RNA Biology · doi:10.1080/15476286.2015.1128065 · Cited by 1,255
Illuminating the silence: understanding the structure and function of small RNAs
Rana, T. M. (2007) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2085 · Cited by 1,083
3′ UTR seed matches, but not overall identity, are associated with RNAi off-targets
Birmingham, A., Anderson, E. M., Reynolds, A., Ilsley-Tyree, D., Leake, D., Fedorov, Y., Baskerville, S., Maksimova, E., Robinson, K., Karpilow, J., et al. (2006) · Nature Methods · doi:10.1038/nmeth854 · Cited by 920
PIK3CA Mutations and Copy Number Gains in Human Lung Cancers
Yamamoto, H., Shigematsu, H., Nomura, M., Lockwood, W. W., Sato, M., Okumura, N., Soh, J., Suzuki, M., Wistuba, I. I., Fong, K. M., et al. (2008) · Cancer Research · doi:10.1158/0008-5472.can-07-5084 · Cited by 429
Sugimoto, K., Ishibashi, T., Sawamura, T., Inoue, N., Kamioka, M., Uekita, H., Ohkawara, H., Sakamoto, T., Sakamoto, N., Okamoto, Y., et al. (2009) · Cardiovascular Research · doi:10.1093/cvr/cvp177 · Cited by 124
Metadata
- Authors
- Naito, Y., Yamada, T., Ui-Tei, K., Morishita, S., & Saigo, K.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2004-07-01
- Volume
- 32
- Issue
- Web Server
- Pages
- W124-W129
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2129205448
- Cited by
- 293
- References
- 21
- FWCI
- 9.51
- Type
- journal article
- Language
- en
- Open access
- hybrid
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- Naito, Y., Yamada, T., Ui-Tei, K., Morishita, S., & Saigo, K. (2004). siDirect: highly effective, target-specific siRNA design software for mammalian RNA interference. Nucleic Acids Research. https://doi.org/10.1093/nar/gkh442
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
