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Items: 1 to 20 of 84

1.

A study of accessible motifs and RNA folding complexity.

Wexler Y, Zilberstein C, Ziv-Ukelson M.

J Comput Biol. 2007 Jul-Aug;14(6):856-72.

PMID:
17691898
2.

A faster algorithm for simultaneous alignment and folding of RNA.

Ziv-Ukelson M, Gat-Viks I, Wexler Y, Shamir R.

J Comput Biol. 2010 Aug;17(8):1051-65. doi: 10.1089/cmb.2009.0197.

PMID:
20649420
3.

Computational prediction of RNA structural motifs involved in post-transcriptional regulatory processes.

Rabani M, Kertesz M, Segal E.

Methods Mol Biol. 2011;714:467-79. doi: 10.1007/978-1-61779-005-8_28.

PMID:
21431758
4.

Practicality and time complexity of a sparsified RNA folding algorithm.

Dimitrieva S, Bucher P.

J Bioinform Comput Biol. 2012 Apr;10(2):1241007. doi: 10.1142/S0219720012410077.

PMID:
22809342
5.
6.
7.

Rnall: an efficient algorithm for predicting RNA local secondary structural landscape in genomes.

Wan XF, Lin G, Xu D.

J Bioinform Comput Biol. 2006 Oct;4(5):1015-31.

PMID:
17099939
8.

Novel and efficient RNA secondary structure prediction using hierarchical folding.

Jabbari H, Condon A, Zhao S.

J Comput Biol. 2008 Mar;15(2):139-63. doi: 10.1089/cmb.2007.0198.

PMID:
18312147
9.

ProbKnot: fast prediction of RNA secondary structure including pseudoknots.

Bellaousov S, Mathews DH.

RNA. 2010 Oct;16(10):1870-80. doi: 10.1261/rna.2125310.

11.

The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data.

Parisien M, Major F.

Nature. 2008 Mar 6;452(7183):51-5. doi: 10.1038/nature06684.

PMID:
18322526
12.
13.

INFO-RNA--a fast approach to inverse RNA folding.

Busch A, Backofen R.

Bioinformatics. 2006 Aug 1;22(15):1823-31.

PMID:
16709587
14.

Consensus folding of unaligned RNA sequences revisited.

Bafna V, Tang H, Zhang S.

J Comput Biol. 2006 Mar;13(2):283-95.

PMID:
16597240
15.

Efficient alignment of RNA secondary structures using sparse dynamic programming.

Zhong C, Zhang S.

BMC Bioinformatics. 2013 Sep 8;14:269. doi: 10.1186/1471-2105-14-269.

16.

Discovering cis-regulatory RNAs in Shewanella genomes by Support Vector Machines.

Xu X, Ji Y, Stormo GD.

PLoS Comput Biol. 2009 Apr;5(4):e1000338. doi: 10.1371/journal.pcbi.1000338.

17.

RNAslider: a faster engine for consecutive windows folding and its application to the analysis of genomic folding asymmetry.

Horesh Y, Wexler Y, Lebenthal I, Ziv-Ukelson M, Unger R.

BMC Bioinformatics. 2009 Mar 4;10:76. doi: 10.1186/1471-2105-10-76.

18.

RADAR: a web server for RNA data analysis and research.

Khaladkar M, Bellofatto V, Wang JT, Tian B, Shapiro BA.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W300-4.

19.

Dynamic programming algorithms for RNA structure prediction with binding sites.

Poolsap U, Kato Y, Akutsu T.

Pac Symp Biocomput. 2010:98-107.

20.

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.

PMID:
23600819

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