RNAhybrid: microRNA target prediction easy, fast and flexible

Krüger J, Rehmsmeier M (2006)
Nucleic Acids Research 34(Web Server): W451-W454.

Journal Article | Original Article | Published | English
In the elucidation of the microRNA regulatory network, knowledge of potential targets is of highest importance. Among existing target prediction methods, RNAhybrid [ M. Rehmsmeier, P. Steffen, M. Hochsmann and R. Giegerich ( 2004) RNA, 10, 1507 - 1517] is unique in offering a flexible online prediction. Recently, some useful features have been added, among these the possibility to disallow G: U base pairs in the seed region, and a seed- match speed- up, which accelerates the program by a factor of 8. In addition, the program can now be used as a webservice for remote calls from user-implemented programs. We demonstrate RNAhybrid's flexibility with the prediction of a non- canonical target site for Caenorhabditis elegans miR- 241 in the 30- untranslated region of lin-39. RNAhybrid is available at http://bibiserv.techfak.uni-bielefeld.de/rnahybrid.
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Krüger J, Rehmsmeier M. RNAhybrid: microRNA target prediction easy, fast and flexible. Nucleic Acids Research. 2006;34(Web Server):W451-W454.
Krüger, J., & Rehmsmeier, M. (2006). RNAhybrid: microRNA target prediction easy, fast and flexible. Nucleic Acids Research, 34(Web Server), W451-W454. doi:10.1093/nar/gkl243
Krüger, J., and Rehmsmeier, M. (2006). RNAhybrid: microRNA target prediction easy, fast and flexible. Nucleic Acids Research 34, W451-W454.
Krüger, J., & Rehmsmeier, M., 2006. RNAhybrid: microRNA target prediction easy, fast and flexible. Nucleic Acids Research, 34(Web Server), p W451-W454.
J. Krüger and M. Rehmsmeier, “RNAhybrid: microRNA target prediction easy, fast and flexible”, Nucleic Acids Research, vol. 34, 2006, pp. W451-W454.
Krüger, J., Rehmsmeier, M.: RNAhybrid: microRNA target prediction easy, fast and flexible. Nucleic Acids Research. 34, W451-W454 (2006).
Krüger, Jan, and Rehmsmeier, Marc. “RNAhybrid: microRNA target prediction easy, fast and flexible”. Nucleic Acids Research 34.Web Server (2006): W451-W454.
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353 Citations in Europe PMC

Data provided by Europe PubMed Central.

Network Properties for Ranking Predicted miRNA Targets in Breast Cancer.
Linde J, Olsson B, Lubovac Z., Adv Bioinformatics (), 2009
PMID: 20224638
The impact of small RNAs. Microsymposium on small RNAs.
Obernosterer G, Meister G, Poy MN, Kuras A., EMBO Rep. 8(1), 2007
PMID: 17170758

22 References

Data provided by Europe PubMed Central.

microRNAs: tiny regulators with great potential.
Ambros V., Cell 107(7), 2001
PMID: 11779458
Gene regulation by microRNAs.
Carthew RW., Curr. Opin. Genet. Dev. 16(2), 2006
PMID: 16503132
miRBase: microRNA sequences, targets and gene nomenclature.
Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ., Nucleic Acids Res. 34(Database issue), 2006
PMID: 16381832
Identification of hundreds of conserved and nonconserved human microRNAs.
Bentwich I, Avniel A, Karov Y, Aharonov R, Gilad S, Barad O, Barzilai A, Einat P, Einav U, Meiri E, Sharon E, Spector Y, Bentwich Z., Nat. Genet. 37(7), 2005
PMID: 15965474
TarBase: A comprehensive database of experimentally supported animal microRNA targets.
Sethupathy P, Corda B, Hatzigeorgiou AG., RNA 12(2), 2006
PMID: 16373484
Prediction of plant microRNA targets.
Rhoades MW, Reinhart BJ, Lim LP, Burge CB, Bartel B, Bartel DP., Cell 110(4), 2002
PMID: 12202040
Prediction of mammalian microRNA targets.
Lewis BP, Shih IH, Jones-Rhoades MW, Bartel DP, Burge CB., Cell 115(7), 2003
PMID: 14697198
Identification of Drosophila MicroRNA targets.
Stark A, Brennecke J, Russell RB, Cohen SM., PLoS Biol. 1(3), 2003
PMID: 14691535
Principles of microRNA-target recognition.
Brennecke J, Stark A, Russell RB, Cohen SM., PLoS Biol. 3(3), 2005
PMID: 15723116
Computational identification of microRNA targets.
Rajewsky N, Socci ND., Dev. Biol. 267(2), 2004
PMID: 15013811
A genome-wide map of conserved microRNA targets in C. elegans.
Lall S, Grun D, Krek A, Chen K, Wang YL, Dewey CN, Sood P, Colombo T, Bray N, Macmenamin P, Kao HL, Gunsalus KC, Pachter L, Piano F, Rajewsky N., Curr. Biol. 16(5), 2006
PMID: 16458514
Human MicroRNA targets.
John B, Enright AJ, Aravin A, Tuschl T, Sander C, Marks DS., PLoS Biol. 2(11), 2004
PMID: 15502875
A combined computational-experimental approach predicts human microRNA targets.
Kiriakidou M, Nelson PT, Kouranov A, Fitziev P, Bouyioukos C, Mourelatos Z, Hatzigeorgiou A., Genes Dev. 18(10), 2004
PMID: 15131085
Fast and effective prediction of microRNA/target duplexes.
Rehmsmeier M, Steffen P, Hochsmann M, Giegerich R., RNA 10(10), 2004
PMID: 15383676
Micro-RNAs: small is plentiful.
Grosshans H, Slack FJ., J. Cell Biol. 156(1), 2002
PMID: 11781331
miRU: an automated plant miRNA target prediction server.
Zhang Y., Nucleic Acids Res. 33(Web Server issue), 2005
PMID: 15980567
The let-7 MicroRNA family members mir-48, mir-84, and mir-241 function together to regulate developmental timing in Caenorhabditis elegans.
Abbott AL, Alvarez-Saavedra E, Miska EA, Lau NC, Bartel DP, Horvitz HR, Ambros V., Dev. Cell 9(3), 2005
PMID: 16139228
The Caenorhabditis elegans homeobox gene cluster.
Burglin TR, Ruvkun G., Curr. Opin. Genet. Dev. 3(4), 1993
PMID: 7902148


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