Literature DB >> 14960474

Gene specific siRNA selector.

Natasha Levenkova1, Qingjuan Gu, John J Rux.   

Abstract

Small interfering RNA (siRNA) is used in functional genomics applications to decrease the expression of a target gene, which may yield a biological effect that suggests a function for the target gene. The siRNA design tool scans a target gene for candidate siRNA sequences that satisfy user-adjustable rules. Selected candidates are then screened to identify those siRNA sequences that are specific to the gene of interest.

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Year:  2004        PMID： 14960474     DOI： 10.1093/bioinformatics/btg437

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  12 in total

1.  siDirect: highly effective, target-specific siRNA design software for mammalian RNA interference.

Authors:  Yuki Naito; Tomoyuki Yamada; Kumiko Ui-Tei; Shinichi Morishita; Kaoru Saigo
Journal:  Nucleic Acids Res       Date:  2004-07-01       Impact factor: 16.971

2.  Lmo genes regulate behavioral responses to ethanol in Drosophila melanogaster and the mouse.

Authors:  Amy W Lasek; Francesco Giorgetti; Karen H Berger; Stacy Tayor; Ulrike Heberlein
Journal:  Alcohol Clin Exp Res       Date:  2011-05-20       Impact factor: 3.455

3.  Energy profile and secondary structure impact shRNA efficacy.

Authors:  Hong Zhou; Xiao Zeng
Journal:  BMC Genomics       Date:  2009-07-07       Impact factor: 3.969

4.  Multi-task learning for cross-platform siRNA efficacy prediction: an in-silico study.

Authors:  Qi Liu; Qian Xu; Vincent W Zheng; Hong Xue; Zhiwei Cao; Qiang Yang
Journal:  BMC Bioinformatics       Date:  2010-04-10       Impact factor: 3.169

5.  MELTING, a flexible platform to predict the melting temperatures of nucleic acids.

Authors:  Marine Dumousseau; Nicolas Rodriguez; Nick Juty; Nicolas Le Novère
Journal:  BMC Bioinformatics       Date:  2012-05-16       Impact factor: 3.169

6.  Genome-wide selection of unique and valid oligonucleotides.

Authors:  Heikki Hyyrö; Martti Juhola; Mauno Vihinen
Journal:  Nucleic Acids Res       Date:  2005-07-26       Impact factor: 16.971

7.  siDirect 2.0: updated software for designing functional siRNA with reduced seed-dependent off-target effect.

Authors:  Yuki Naito; Jun Yoshimura; Shinichi Morishita; Kumiko Ui-Tei
Journal:  BMC Bioinformatics       Date:  2009-11-30       Impact factor: 3.169

8.  Regression of murine lung tumors by the let-7 microRNA.

Authors:  P Trang; P P Medina; J F Wiggins; L Ruffino; K Kelnar; M Omotola; R Homer; D Brown; A G Bader; J B Weidhaas; F J Slack
Journal:  Oncogene       Date:  2009-12-07       Impact factor: 9.867

9.  Whole-genome thermodynamic analysis reduces siRNA off-target effects.

Authors:  Xi Chen; Peng Liu; Hui-Hsien Chou
Journal:  PLoS One       Date:  2013-03-06       Impact factor: 3.240

10.  Comparison of approaches for rational siRNA design leading to a new efficient and transparent method.

Authors:  Olga Matveeva; Yury Nechipurenko; Leo Rossi; Barry Moore; Pål Saetrom; Aleksey Y Ogurtsov; John F Atkins; Svetlana A Shabalina
Journal:  Nucleic Acids Res       Date:  2007-04-10       Impact factor: 16.971
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