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Items: 1 to 20 of 24

1.

Efficient siRNA selection using hybridization thermodynamics.

Lu ZJ, Mathews DH.

Nucleic Acids Res. 2008 Feb;36(2):640-7. Epub 2007 Dec 10.

2.
3.

A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation.

Lu ZJ, Turner DH, Mathews DH.

Nucleic Acids Res. 2006;34(17):4912-24. Epub 2006 Sep 18.

4.

Computational models with thermodynamic and composition features improve siRNA design.

Shabalina SA, Spiridonov AN, Ogurtsov AY.

BMC Bioinformatics. 2006 Feb 12;7:65.

5.

Design of a genome-wide siRNA library using an artificial neural network.

Huesken D, Lange J, Mickanin C, Weiler J, Asselbergs F, Warner J, Meloon B, Engel S, Rosenberg A, Cohen D, Labow M, Reinhardt M, Natt F, Hall J.

Nat Biotechnol. 2005 Aug;23(8):995-1001. Epub 2005 Jul 17. Erratum in: Nat Biotechnol. 2005 Oct;23(10):1315. Nat Biotechnol. 2006 Aug;24(8):1033.

PMID:
16025102
6.

Local RNA target structure influences siRNA efficacy: systematic analysis of intentionally designed binding regions.

Schubert S, Grünweller A, Erdmann VA, Kurreck J.

J Mol Biol. 2005 May 13;348(4):883-93.

PMID:
15843020
7.

siRNA target site secondary structure predictions using local stable substructures.

Heale BS, Soifer HS, Bowers C, Rossi JJ.

Nucleic Acids Res. 2005 Feb 18;33(3):e30. Erratum in: Nucleic Acids Res. 2006;34(16):4653.

8.

A comparison of siRNA efficacy predictors.

Saetrom P, Snøve O Jr.

Biochem Biophys Res Commun. 2004 Aug 13;321(1):247-53.

PMID:
15358242
10.

siRNA Selection Server: an automated siRNA oligonucleotide prediction server.

Yuan B, Latek R, Hossbach M, Tuschl T, Lewitter F.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W130-4.

11.

Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure.

Mathews DH, Disney MD, Childs JL, Schroeder SJ, Zuker M, Turner DH.

Proc Natl Acad Sci U S A. 2004 May 11;101(19):7287-92. Epub 2004 May 3.

12.

An algorithm for selection of functional siRNA sequences.

Amarzguioui M, Prydz H.

Biochem Biophys Res Commun. 2004 Apr 16;316(4):1050-8.

PMID:
15044091
13.

Guidelines for the selection of highly effective siRNA sequences for mammalian and chick RNA interference.

Ui-Tei K, Naito Y, Takahashi F, Haraguchi T, Ohki-Hamazaki H, Juni A, Ueda R, Saigo K.

Nucleic Acids Res. 2004 Feb 9;32(3):936-48. Print 2004.

14.

Rational siRNA design for RNA interference.

Reynolds A, Leake D, Boese Q, Scaringe S, Marshall WS, Khvorova A.

Nat Biotechnol. 2004 Mar;22(3):326-30. Epub 2004 Feb 1.

15.

Approaches for the sequence-specific knockdown of mRNA.

Scherer LJ, Rossi JJ.

Nat Biotechnol. 2003 Dec;21(12):1457-65. Review.

PMID:
14647331
16.

Functional siRNAs and miRNAs exhibit strand bias.

Khvorova A, Reynolds A, Jayasena SD.

Cell. 2003 Oct 17;115(2):209-16. Erratum in: Cell. 2003 Nov 14;115(4):505.

17.

Asymmetry in the assembly of the RNAi enzyme complex.

Schwarz DS, Hutvágner G, Du T, Xu Z, Aronin N, Zamore PD.

Cell. 2003 Oct 17;115(2):199-208.

18.
19.

Sequence, chemical, and structural variation of small interfering RNAs and short hairpin RNAs and the effect on mammalian gene silencing.

Harborth J, Elbashir SM, Vandenburgh K, Manninga H, Scaringe SA, Weber K, Tuschl T.

Antisense Nucleic Acid Drug Dev. 2003 Apr;13(2):83-105.

PMID:
12804036
20.

The efficacy of small interfering RNAs targeted to the type 1 insulin-like growth factor receptor (IGF1R) is influenced by secondary structure in the IGF1R transcript.

Bohula EA, Salisbury AJ, Sohail M, Playford MP, Riedemann J, Southern EM, Macaulay VM.

J Biol Chem. 2003 May 2;278(18):15991-7. Epub 2003 Feb 24.

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