Efficient prediction methods for selecting effective siRNA sequences

Fire, 1998, Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans, Nature, 391, 806, 10.1038/35888 Sharp, 2001, RNA interference–2001, Genes Dev., 15, 485, 10.1101/gad.880001 Elbashir, 2001, Duplexes of 21-nucleotide RNAs mediate RNA interference in mammalian cell culture, Nature, 411, 494, 10.1038/35078107 Elbashir, 2001, RNA interference is mediated by 21- and 22-nucleotide RNAs, Genes Dev., 15, 188, 10.1101/gad.862301 Dykxhoorn, 2003, Killing the messenger: short RNAs that silence gene expression, Nature Review, 4, 457, 10.1038/nrm1129 Hannon, 2002, RNA interference, Nature, 418, 244, 10.1038/418244a Holen, 2002, Positional effects of short interfering RNAs targeting the human coagulation trigger tissue factor, Nucleic Acids Res., 30, 1757, 10.1093/nar/30.8.1757 Elbashir, 2001, Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate, EMBO J., 20, 6877, 10.1093/emboj/20.23.6877 Kumar, 2003, High-throughput selection of effective RNAi probes for gene silencing, Genome Res., 13, 2333, 10.1101/gr.1575003 Mittal, 2004, Improving the efficiency of RNA interference in mammals, Nature Rev. Genetics, 5, 355, 10.1038/nrg1323 Schwarz, 2003, Asymmetry in the assembly of the RNAi enzyme complex, Cell, 115, 199, 10.1016/S0092-8674(03)00759-1 Khvorova, 2003, Functional siRNAs and miRNAs exhibit strand bias, Cell, 115, 209, 10.1016/S0092-8674(03)00801-8 Chalk, 2004, Improved and automated prediction of effective siRNA, Biochem. Biophys. Res. Commun., 319, 264, 10.1016/j.bbrc.2004.04.181 Teramoto, 2005, Prediction of siRNA functionality using generalized string kernel and support vector machine, FEBS Letters, 579, 2878, 10.1016/j.febslet.2005.04.045 Naito, 2004, siDirect: highly effective, target-specific siRNA design software for mammalian RNA interference, Nucleic Acids Res., 32, W124, 10.1093/nar/gkh442 Santoyo, 2004, Highly specific and accurate selection of siRNAs for high-throughput functional assays, Bioinformatics, 21, 1376, 10.1093/bioinformatics/bti196 Truss, 2005, HuSiDa—the human siRNA database: an open-access database for published functional siRNA sequences and technical details of efficient transfer into recipient cells, Nucleic Acids Res., 33, D108, 10.1093/nar/gki131 Reynolds, 2004, Rational siRNA design for RNA interference, Nat. Biotech., 22, 326, 10.1038/nbt936 Ui-Tei, 2004, Guidelines for the selection of highly effective siRNA sequences for mammalian and chick RNA interference, Nucleic Acids Res., 32, 936, 10.1093/nar/gkh247 Amarzguioui, 2004, An algorithm for selection of functional siRNA sequences, Biochem. Biophys. Res. Commun., 316, 1050, 10.1016/j.bbrc.2004.02.157 Hsieh, 2004, A library of siRNA duplexes targeting the phosphoinositide 3-kinase pathway: determinants of gene silencing for use in cell-based screens, Nucleic Acids Res., 32, 893, 10.1093/nar/gkh238 Jagla, 2005, Sequence characteristics of functional siRNAs, RNA, 11, 864, 10.1261/rna.7275905 Huesken, 2005, Design of a genome-wide siRNA library using an artificial neural network, Nat. Biotech., 23, 995, 10.1038/nbt1118 Snove, 2004, Designing effective siRNAs with off-target control, Biochem. Biophy. Res. Commun., 325, 769, 10.1016/j.bbrc.2004.10.097 Poggio, 1990, Networks for approximation and learning, Proc. of IEEE, 78, 1481, 10.1109/5.58326 Wu, 2000 Takasaki, 2006, Selecting effective siRNA sequences by using radial basis function network and decision tree learning, BMC Bioinformatics, 7, S22, 10.1186/1471-2105-7-S5-S22 Takasaki, 2004, An effective method for selecting siRNA target sequences in mammalian cells, Cell Cycle, 3, 790, 10.4161/cc.3.6.892 Takasaki, 2005, Selecting effective siRNA target sequences for mammalian genes, RNA Biology, 2, 21, 10.4161/rna.2.1.1404 Takasaki, 2006, Selecting effective siRNA sequences based on the self-organizing map and statistical techniques, Comput. Biol. Chem., 30, 169, 10.1016/j.compbiolchem.2006.02.003 Takasaki, 2006, Comparative analyses for selecting effective siRNA sequences, Chem-Bio Informatics J., 6, 69, 10.1273/cbij.6.69 Saetrom, 2004, A comparison of siRNA efficacy predictors, Biochem. Biophy. Res. Commun., 321, 247, 10.1016/j.bbrc.2004.06.116 Ladunga, 2007, More complete gene silencing by fewer siRNAs: transparent optimized design and biophysical signature, Nucleic Acids Res., 35, 433, 10.1093/nar/gkl1065 Holen, 2006, Efficient prediction of siRNAs with siRNArules 1.0: an open-source JAVA approach to siRNA algorithms, RNA, 12, 1620, 10.1261/rna.81006 Saetrom, 2004, Predicting the efficacy of short oligonucleotides in antisense and RNAi experiments with boosted genetic programming, Bioinformatics, 20, 3055, 10.1093/bioinformatics/bth364 Heale, 2005, siRNA target site secondary structure predictions using local stable substructures, Nucleic Acids Res., 33, e-30, 10.1093/nar/gni026 Luo, 2004, The gene-silencing efficacy of siRNA is strongly dependent on the local structure of mRNA at the target region, Biochem. Biophy. Res. Commun., 318, 303, 10.1016/j.bbrc.2004.04.027 Bohula, 2003, The efficacy of small interfering RNAs targeted to the type I insulin-like growth factor receptor (IGFIR) is influenced by secondary structure in the IGFIR transcript, J. Biol. Chem., 278, 15991, 10.1074/jbc.M300714200 Elbashir, 2002, Analysis of gene function in somatic mammalian cells using small interfering RNAs, Methods, 26, 199, 10.1016/S1046-2023(02)00023-3 Quinlan, 1986, Induction of decision tree, Machine Learning, 1, 81, 10.1007/BF00116251 Metz, 1998, Statistical comparison of two ROC-curve estimates obtained from partially-paired datasets, Med. Decis. Making, 18, 110, 10.1177/0272989X9801800118