PubMed

Analysis by siRNA_profile program displays novel thermodynamic characteristics of highly functional siRNA molecules.

Muhonen P, Parthasarathy RN, Janckila AJ, Büki KG, Väänänen HK.

Source Code Biol Med. 2008 May 21;3:8.PMID: 18495017 [PubMed - in process]Related articlesFree article

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

Naito Y, Yoshimura J, Morishita S, Ui-Tei K.

BMC Bioinformatics. 2009 Nov 30;10:392.PMID: 19948054 [PubMed - indexed for MEDLINE]Related articlesFree article

Batch RNAi selector: a standalone program to predict specific siRNA candidates in batches with enhanced sensitivity.

Iyer S, Deutsch K, Yan X, Lin B.

Comput Methods Programs Biomed. 2007 Mar;85(3):203-9. Epub 2007 Jan 2.PMID: 17197051 [PubMed - indexed for MEDLINE]Related articles

Functional characterization of endogenous siRNA target genes in Caenorhabditis elegans.

Asikainen S, Heikkinen L, Wong G, Storvik M.

BMC Genomics. 2008 Jun 3;9:270.PMID: 18522735 [PubMed - indexed for MEDLINE]Related articlesFree article

Bioinformatic Approaches to siRNA Selection and Optimization.

Muhonen P, Holthofer H.

Methods Mol Biol. 2010;623:93-107.PMID: 20217546 [PubMed - in process]Related articles

Asymmetric shorter-duplex siRNA structures trigger efficient gene silencing with reduced nonspecific effects.

Chang CI, Yoo JW, Hong SW, Lee SE, Kang HS, Sun X, Rogoff HA, Ban C, Kim S, Li CJ, Lee DK.

Mol Ther. 2009 Apr;17(4):725-32. Epub 2009 Jan 20.PMID: 19156133 [PubMed - indexed for MEDLINE]Related articles

Design and validation of siRNAs and shRNAs.

Tilesi F, Fradiani P, Socci V, Willems D, Ascenzioni F.

Curr Opin Mol Ther. 2009 Apr;11(2):156-64. Review.PMID: 19330721 [PubMed - indexed for MEDLINE]Related articles

Effect of asymmetric terminal structures of short RNA duplexes on the RNA interference activity and strand selection.

Sano M, Sierant M, Miyagishi M, Nakanishi M, Takagi Y, Sutou S.

Nucleic Acids Res. 2008 Oct;36(18):5812-21. Epub 2008 Sep 9.PMID: 18782830 [PubMed - indexed for MEDLINE]Related articlesFree article

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

Matveeva O, Nechipurenko Y, Rossi L, Moore B, Saetrom P, Ogurtsov AY, Atkins JF, Shabalina SA.

Nucleic Acids Res. 2007;35(8):e63. Epub 2007 Apr 10.PMID: 17426130 [PubMed - indexed for MEDLINE]Related articlesFree article

Off-target effects of siRNA specific for GFP.

Tschuch C, Schulz A, Pscherer A, Werft W, Benner A, Hotz-Wagenblatt A, Barrionuevo LS, Lichter P, Mertens D.

BMC Mol Biol. 2008 Jun 24;9:60.PMID: 18577207 [PubMed - indexed for MEDLINE]Related articlesFree article

Potent RNAi by short RNA triggers.

Chu CY, Rana TM.

RNA. 2008 Sep;14(9):1714-9. Epub 2008 Jul 24.PMID: 18658119 [PubMed - indexed for MEDLINE]Related articlesFree article

Analysis of Putative miRNA-Binding Sites and mRNA 3'Ends as Targets for siRNA-Mediated Gene Knockdown.

Bergauer T, Krueger U, Lader E, Pilk S, Wolter I, Bielke W.

Oligonucleotides. 2009 Jan 28. [Epub ahead of print]PMID: 19196098 [PubMed - as supplied by publisher]Related articles

The efficiency of CD40 down regulation by siRNA and antisense ODN: comparison of lipofectamine and FuGENE6.

Ebadi P, Karimi MH, Pourfathollah AA, Saheb Ghadam Lotfi A, Soheili ZS, Samiee S, Hajati S, Nadali F, Geramizadeh B, Moazzeni SM.

Iran J Immunol. 2009 Mar;6(1):1-11.PMID: 19293472 [PubMed - indexed for MEDLINE]Related articles

Optimal design and validation of antiviral siRNA for targeting hepatitis B virus.

Fu J, Tang ZM, Gao X, Zhao F, Zhong H, Wen MR, Sun X, Song HF, Qian XH.

Acta Pharmacol Sin. 2008 Dec;29(12):1522-8.PMID: 19026173 [PubMed - indexed for MEDLINE]Related articlesFree article

Methods for selecting effective siRNA sequences by using statistical and clustering techniques.

Takasaki S.

Methods Mol Biol. 2009;487:1-39. Review.PMID: 19301640 [PubMed - indexed for MEDLINE]Related articles

A direct phenotypic comparison of siRNA pools and multiple individual duplexes in a functional assay.

Parsons BD, Schindler A, Evans DH, Foley E.

PLoS One. 2009 Dec 29;4(12):e8471.PMID: 20041186 [PubMed - in process]Related articlesFree article

Energy profile and secondary structure impact shRNA efficacy.

Zhou H, Zeng X.

BMC Genomics. 2009 Jul 7;10 Suppl 1:S9.PMID: 19594886 [PubMed - indexed for MEDLINE]Related articlesFree article

Designing and utilization of siRNAs targeting RNA binding proteins.

Kim DH, Behlke M, Rossi JJ.

Methods Mol Biol. 2008;488:367-81.PMID: 18982303 [PubMed - indexed for MEDLINE]Related articles

Selecting effective siRNA target sequences by using Bayes' theorem.

Takasaki S.

Comput Biol Chem. 2009 Oct;33(5):368-72. Epub 2009 Jul 19.PMID: 19682951 [PubMed - indexed for MEDLINE]Related articles

Graft Protection in Bypass Surgery: siRNA-Mediated Silencing of Adhesion Molecules.

Walker T, Wendel HP, Raabe C, Wyechnik P, Spranger L, Heidenreich O, Scheule AM, Nordheim A, Ziemer G.

Oligonucleotides. 2009 Jan 6. [Epub ahead of print]PMID: 19125637 [PubMed - as supplied by publisher]Related articles