A comparison of siRNA efficacy predictors

Created by W.Langdon from gp-bibliography.bib Revision:1.4221

  author =       "Pal Saetrom and Ola {Snove, Jr.}",
  title =        "A comparison of siRNA efficacy predictors",
  journal =      "Biochemical and Biophysical Research Communications",
  year =         "2004",
  volume =       "321",
  pages =        "247--253",
  number =       "1",
  abstract =     "Short interfering RNA (siRNA) efficacy prediction
                 algorithms aim to increase the probability of selecting
                 target sites that are applicable for gene silencing by
                 RNA interference. Many algorithms have been published
                 recently, and they base their predictions on such
                 different features as duplex stability, sequence
                 characteristics, mRNA secondary structure, and target
                 site uniqueness. We compare the performance of the
                 algorithms on a collection of publicly available
                 siRNAs. First, we show that our regularised genetic
                 programming algorithm GPboost appears to have a higher
                 and more stable performance than other algorithms on
                 the collected datasets. Second, several algorithms gave
                 close to random classification on unseen data, and only
                 GPboost and three other algorithms have a reasonably
                 high and stable performance on all parts of the
                 dataset. Third, the results indicate that the siRNAs'
                 sequence is sufficient input to siRNA efficacy
                 algorithms, and that other features that have been
                 suggested to be important may be indirectly captured by
                 the sequence.",
  owner =        "wlangdon",
  URL =          "http://www.sciencedirect.com/science/article/B6WBK-4CW546Y-S/2/1c4d9091ea50571084790a39c8ff0b81",
  month =        "13 " # aug,
  keywords =     "genetic algorithms, genetic programming",
  DOI =          "doi:10.1016/j.bbrc.2004.06.116",
  notes =        "PMID: 15358242

                 Cited by Demonstration of two novel methods for
                 predicting functional siRNA efficiency Peilin Jia,
                 Tieliu Shi, Yudong Cai, and Yixue Li BMC
                 Bioinformatics. 2006; 7: 271. Published online 2006 May
                 29. doi:10.1186/1471-2105-7-271. PMCID: PMC1524998",

Genetic Programming entries for Pal Saetrom Ola Snove Jr