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Results: 1 to 20 of 105

1.

A global sampling approach to designing and reengineering RNA secondary structures.

Levin A, Lis M, Ponty Y, O'Donnell CW, Devadas S, Berger B, Waldispühl J.

Nucleic Acids Res. 2012 Nov 1;40(20):10041-52. doi: 10.1093/nar/gks768. Epub 2012 Aug 31.

PMID:
22941632
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotide distribution.

Reinharz V, Ponty Y, Waldispühl J.

Bioinformatics. 2013 Jul 1;29(13):i308-15. doi: 10.1093/bioinformatics/btt217.

PMID:
23812999
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Frnakenstein: multiple target inverse RNA folding.

Lyngsø RB, Anderson JW, Sizikova E, Badugu A, Hyland T, Hein J.

BMC Bioinformatics. 2012 Oct 9;13:260. doi: 10.1186/1471-2105-13-260.

PMID:
23043260
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

An unbiased adaptive sampling algorithm for the exploration of RNA mutational landscapes under evolutionary pressure.

Waldispühl J, Ponty Y.

J Comput Biol. 2011 Nov;18(11):1465-79. doi: 10.1089/cmb.2011.0181. Epub 2011 Oct 28.

PMID:
22035326
[PubMed - indexed for MEDLINE]
5.

RNAiFOLD: a constraint programming algorithm for RNA inverse folding and molecular design.

Garcia-Martin JA, Clote P, Dotu I.

J Bioinform Comput Biol. 2013 Apr;11(2):1350001. doi: 10.1142/S0219720013500017. Epub 2013 Feb 6.

PMID:
23600819
[PubMed - indexed for MEDLINE]
6.

A new algorithm for RNA secondary structure design.

Andronescu M, Fejes AP, Hutter F, Hoos HH, Condon A.

J Mol Biol. 2004 Feb 20;336(3):607-24.

PMID:
15095976
[PubMed - indexed for MEDLINE]
7.

Efficient algorithms for probing the RNA mutation landscape.

Waldispühl J, Devadas S, Berger B, Clote P.

PLoS Comput Biol. 2008 Aug 8;4(8):e1000124. doi: 10.1371/journal.pcbi.1000124.

PMID:
18688270
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Computing the partition function for kinetically trapped RNA secondary structures.

Lorenz WA, Clote P.

PLoS One. 2011 Jan 28;6(1):e16178. doi: 10.1371/journal.pone.0016178.

PMID:
21297972
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Evaluation of a sophisticated SCFG design for RNA secondary structure prediction.

Nebel ME, Scheid A.

Theory Biosci. 2011 Dec;130(4):313-36. doi: 10.1007/s12064-011-0139-7. Epub 2011 Dec 2.

PMID:
22135038
[PubMed - indexed for MEDLINE]
10.

Crumple: a method for complete enumeration of all possible pseudoknot-free RNA secondary structures.

Bleckley S, Stone JW, Schroeder SJ.

PLoS One. 2012;7(12):e52414. doi: 10.1371/journal.pone.0052414. Epub 2012 Dec 27.

PMID:
23300665
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Finding stable local optimal RNA secondary structures.

Li Y, Zhang S.

Bioinformatics. 2011 Nov 1;27(21):2994-3001. doi: 10.1093/bioinformatics/btr510. Epub 2011 Sep 8.

PMID:
21903624
[PubMed - indexed for MEDLINE]
Free Article
12.

A statistical sampling algorithm for RNA secondary structure prediction.

Ding Y, Lawrence CE.

Nucleic Acids Res. 2003 Dec 15;31(24):7280-301.

PMID:
14654704
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

RNAexinv: An extended inverse RNA folding from shape and physical attributes to sequences.

Avihoo A, Churkin A, Barash D.

BMC Bioinformatics. 2011 Aug 3;12:319. doi: 10.1186/1471-2105-12-319.

PMID:
21813013
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

corRna: a web server for predicting multiple-point deleterious mutations in structural RNAs.

Lam E, Kam A, Waldispühl J.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W160-6. doi: 10.1093/nar/gkr358. Epub 2011 May 19.

PMID:
21596778
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Paradigms for computational nucleic acid design.

Dirks RM, Lin M, Winfree E, Pierce NA.

Nucleic Acids Res. 2004 Feb 27;32(4):1392-403. Print 2004.

PMID:
14990744
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Towards 3D structure prediction of large RNA molecules: an integer programming framework to insert local 3D motifs in RNA secondary structure.

Reinharz V, Major F, Waldispühl J.

Bioinformatics. 2012 Jun 15;28(12):i207-14. doi: 10.1093/bioinformatics/bts226.

PMID:
22689763
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Rchange: algorithms for computing energy changes of RNA secondary structures in response to base mutations.

Kiryu H, Asai K.

Bioinformatics. 2012 Apr 15;28(8):1093-101. doi: 10.1093/bioinformatics/bts097. Epub 2012 Feb 28.

PMID:
22373787
[PubMed - indexed for MEDLINE]
Free Article
18.

Random K-noncrossing RNA structures.

Chen WY, Han HS, Reidys CM.

Proc Natl Acad Sci U S A. 2009 Dec 29;106(52):22061-6. doi: 10.1073/pnas.0907269106. Epub 2009 Dec 11.

PMID:
20018731
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Discretized torsional dynamics and the folding of an RNA chain.

Fernández A, Salthú R, Cendra H.

Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 1999 Aug;60(2 Pt B):2105-19.

PMID:
11970003
[PubMed - indexed for MEDLINE]
20.

An optimized parsing algorithm well suited to RNA folding.

Lefebvre F.

Proc Int Conf Intell Syst Mol Biol. 1995;3:222-30.

PMID:
7584441
[PubMed - indexed for MEDLINE]

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