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Items: 1 to 20 of 104

1.

Expected distance between terminal nucleotides of RNA secondary structures.

Clote P, Ponty Y, Steyaert JM.

J Math Biol. 2012 Sep;65(3):581-99. doi: 10.1007/s00285-011-0467-8.

PMID:
21984358
2.

Asymptotics of canonical and saturated RNA secondary structures.

Clote P, Kranakis E, Krizanc D, Salvy B.

J Bioinform Comput Biol. 2009 Oct;7(5):869-93.

PMID:
19785050
3.

Asymptotic number of hairpins of saturated RNA secondary structures.

Clote P, Kranakis E, Krizanc D.

Bull Math Biol. 2013 Dec;75(12):2410-30. doi: 10.1007/s11538-013-9899-1.

PMID:
24142625
4.

The ends of a large RNA molecule are necessarily close.

Yoffe AM, Prinsen P, Gelbart WM, Ben-Shaul A.

Nucleic Acids Res. 2011 Jan;39(1):292-9. doi: 10.1093/nar/gkq642.

5.

Moments of the Boltzmann distribution for RNA secondary structures.

Miklós I, Meyer IM, Nagy B.

Bull Math Biol. 2005 Sep;67(5):1031-47.

PMID:
15998494
6.

Investigation of the Bernoulli model for RNA secondary structures.

Nebel ME.

Bull Math Biol. 2004 Sep;66(5):925-64.

PMID:
15294413
7.

Combinatorics of locally optimal RNA secondary structures.

Fusy E, Clote P.

J Math Biol. 2014 Jan;68(1-2):341-75. doi: 10.1007/s00285-012-0631-9.

PMID:
23263300
8.

Secondary structure model for the last two domains of single-stranded RNA phage Q beta.

Beekwilder MJ, Nieuwenhuizen R, van Duin J.

J Mol Biol. 1995 Apr 14;247(5):903-17.

PMID:
7723040
9.
10.

Statistics of canonical RNA pseudoknot structures.

Huang FW, Reidys CM.

J Theor Biol. 2008 Aug 7;253(3):570-8. doi: 10.1016/j.jtbi.2008.04.002.

PMID:
18511081
11.

RNA secondary structures in a polymer-zeta model how foldings should be shaped for sparsification to establish a linear speedup.

Jin EY, Nebel ME.

J Math Biol. 2016 Feb;72(3):527-71. doi: 10.1007/s00285-015-0894-z.

PMID:
26001743
12.

The 5'-3' distance of RNA secondary structures.

Han HS, Reidys CM.

J Comput Biol. 2012 Jul;19(7):867-78. doi: 10.1089/cmb.2011.0301.

PMID:
22731624
13.

The end-to-end distance of RNA as a randomly self-paired polymer.

Fang LT.

J Theor Biol. 2011 Jul 7;280(1):101-7. doi: 10.1016/j.jtbi.2011.04.010.

PMID:
21515288
14.

Maximum expected accuracy structural neighbors of an RNA secondary structure.

Clote P, Lou F, Lorenz WA.

BMC Bioinformatics. 2012 Apr 12;13 Suppl 5:S6. doi: 10.1186/1471-2105-13-S5-S6.

15.

A sequential folding model predicts length-independent secondary structure properties of long ssRNA.

Fang LT, Yoffe AM, Gelbart WM, Ben-Shaul A.

J Phys Chem B. 2011 Mar 31;115(12):3193-9. doi: 10.1021/jp110680e.

PMID:
21370842
16.
17.

Dynalign: an algorithm for finding the secondary structure common to two RNA sequences.

Mathews DH, Turner DH.

J Mol Biol. 2002 Mar 22;317(2):191-203.

PMID:
11902836
18.

Memory efficient folding algorithms for circular RNA secondary structures.

Hofacker IL, Stadler PF.

Bioinformatics. 2006 May 15;22(10):1172-6.

PMID:
16452114
19.

Predicting a set of minimal free energy RNA secondary structures common to two sequences.

Mathews DH.

Bioinformatics. 2005 May 15;21(10):2246-53.

PMID:
15731207
20.

Combinatorics of RNA Secondary Structures with Base Triples.

Müller R, Nebel ME.

J Comput Biol. 2015 Jul;22(7):619-48. doi: 10.1089/cmb.2013.0022.

PMID:
26098199
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