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Results: 1 to 20 of 45

1.

Energy parameters and novel algorithms for an extended nearest neighbor energy model of RNA.

Dotu I, Mechery V, Clote P.

PLoS One. 2014 Feb 21;9(2):e85412. doi: 10.1371/journal.pone.0085412. eCollection 2014.

PMID:
24586240
[PubMed - in process]
Free PMC Article
2.

Computing the probability of RNA hairpin and multiloop formation.

Ding Y, Lorenz WA, Dotu I, Senter E, Clote P.

J Comput Biol. 2014 Mar;21(3):201-18. doi: 10.1089/cmb.2013.0148. Epub 2014 Feb 21.

PMID:
24559086
[PubMed - in process]
3.

RNA folding pathways and kinetics using 2D energy landscapes.

Senter E, Dotu I, Clote P.

J Math Biol. 2014 Feb 12. [Epub ahead of print]

PMID:
24515409
[PubMed - as supplied by publisher]
4.

Using RNA inverse folding to identify IRES-like structural subdomains.

Dotu I, Lozano G, Clote P, Martinez-Salas E.

RNA Biol. 2013 Dec 1;10(12):1842-52. doi: 10.4161/rna.26994. Epub 2013 Nov 4.

PMID:
24253111
[PubMed - in process]
Free PMC Article
5.

Asymptotic structural properties of quasi-random saturated structures of RNA.

Clote P, Kranakis E, Krizanc D.

Algorithms Mol Biol. 2013 Oct 25;8(1):24. doi: 10.1186/1748-7188-8-24.

PMID:
24156624
[PubMed]
Free PMC Article
6.

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. Epub 2013 Oct 19.

PMID:
24142625
[PubMed - in process]
7.

RNAiFold: a web server for RNA inverse folding and molecular design.

Garcia-Martin JA, Clote P, Dotu I.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W465-70. doi: 10.1093/nar/gkt280. Epub 2013 May 21.

PMID:
23700314
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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]
9.

Using the fast fourier transform to accelerate the computational search for RNA conformational switches.

Senter E, Sheikh S, Dotu I, Ponty Y, Clote P.

PLoS One. 2012;7(12):e50506. doi: 10.1371/journal.pone.0050506. Epub 2012 Dec 19.

PMID:
23284639
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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. Epub 2012 Dec 22.

PMID:
23263300
[PubMed - in process]
11.

Integrating chemical footprinting data into RNA secondary structure prediction.

Zarringhalam K, Meyer MM, Dotu I, Chuang JH, Clote P.

PLoS One. 2012;7(10):e45160. doi: 10.1371/journal.pone.0045160. Epub 2012 Oct 16.

PMID:
23091593
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

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.

PMID:
22537010
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

On the page number of RNA secondary structures with pseudoknots.

Clote P, Dobrev S, Dotu I, Kranakis E, Krizanc D, Urrutia J.

J Math Biol. 2012 Dec;65(6-7):1337-57. doi: 10.1007/s00285-011-0493-6. Epub 2011 Dec 10.

PMID:
22159642
[PubMed - indexed for MEDLINE]
14.

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. Epub 2011 Oct 9.

PMID:
21984358
[PubMed - indexed for MEDLINE]
15.

On lattice protein structure prediction revisited.

Dotu I, Cebrián M, Van Hentenryck P, Clote P.

IEEE/ACM Trans Comput Biol Bioinform. 2011 Nov-Dec;8(6):1620-32. doi: 10.1109/TCBB.2011.41.

PMID:
21358007
[PubMed - indexed for MEDLINE]
16.

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
17.

Fragmentation-free LC-MS can identify hundreds of proteins.

Bochet P, Rügheimer F, Guina T, Brooks P, Goodlett D, Clote P, Schwikowski B.

Proteomics. 2011 Jan;11(1):22-32. doi: 10.1002/pmic.200900765. Epub 2010 Dec 6.

PMID:
21182191
[PubMed - indexed for MEDLINE]
18.

Thermodynamics of RNA structures by Wang-Landau sampling.

Lou F, Clote P.

Bioinformatics. 2010 Jun 15;26(12):i278-86. doi: 10.1093/bioinformatics/btq218.

PMID:
20529917
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Computing folding pathways between RNA secondary structures.

Dotu I, Lorenz WA, Van Hentenryck P, Clote P.

Nucleic Acids Res. 2010 Mar;38(5):1711-22. doi: 10.1093/nar/gkp1054. Epub 2009 Dec 30.

PMID:
20044352
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

RNA structural segmentation.

Dotú I, Lorenz WA, VAN Hentenryck P, Clote P.

Pac Symp Biocomput. 2010:57-68.

PMID:
19908358
[PubMed - indexed for MEDLINE]
Free Article

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