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Results: 17

1.

Characteristics and prediction of RNA structure.

Li H, Zhu D, Zhang C, Han H, Crandall KA.

Biomed Res Int. 2014;2014:690340. doi: 10.1155/2014/690340. Epub 2014 Jul 6.

PMID:
25110687
[PubMed - in process]
Free PMC Article
2.

A fast and robust iterative algorithm for prediction of RNA pseudoknotted secondary structures.

Jabbari H, Condon A.

BMC Bioinformatics. 2014 May 18;15:147. doi: 10.1186/1471-2105-15-147.

PMID:
24884954
[PubMed - in process]
Free PMC Article
3.

Ebola virus RNA editing depends on the primary editing site sequence and an upstream secondary structure.

Mehedi M, Hoenen T, Robertson S, Ricklefs S, Dolan MA, Taylor T, Falzarano D, Ebihara H, Porcella SF, Feldmann H.

PLoS Pathog. 2013;9(10):e1003677. doi: 10.1371/journal.ppat.1003677. Epub 2013 Oct 17.

PMID:
24146620
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

RNAstructure: Web servers for RNA secondary structure prediction and analysis.

Bellaousov S, Reuter JS, Seetin MG, Mathews DH.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W471-4. doi: 10.1093/nar/gkt290. Epub 2013 Apr 24.

PMID:
23620284
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots.

Hajdin CE, Bellaousov S, Huggins W, Leonard CW, Mathews DH, Weeks KM.

Proc Natl Acad Sci U S A. 2013 Apr 2;110(14):5498-503. doi: 10.1073/pnas.1219988110. Epub 2013 Mar 15.

PMID:
23503844
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction.

Puton T, Kozlowski LP, Rother KM, Bujnicki JM.

Nucleic Acids Res. 2013 Apr;41(7):4307-23. doi: 10.1093/nar/gkt101. Epub 2013 Feb 21. Erratum in: Nucleic Acids Res. 2014 Apr;42(8):5403-6.

PMID:
23435231
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

McGenus: a Monte Carlo algorithm to predict RNA secondary structures with pseudoknots.

Bon M, Micheletti C, Orland H.

Nucleic Acids Res. 2013 Feb 1;41(3):1895-900. doi: 10.1093/nar/gks1204. Epub 2012 Dec 16.

PMID:
23248008
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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
9.

Predicting pseudoknotted structures across two RNA sequences.

Sperschneider J, Datta A, Wise MJ.

Bioinformatics. 2012 Dec 1;28(23):3058-65. doi: 10.1093/bioinformatics/bts575. Epub 2012 Oct 8.

PMID:
23044552
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Pregnancy-induced noncoding RNA (PINC) associates with polycomb repressive complex 2 and regulates mammary epithelial differentiation.

Shore AN, Kabotyanski EB, Roarty K, Smith MA, Zhang Y, Creighton CJ, Dinger ME, Rosen JM.

PLoS Genet. 2012;8(7):e1002840. doi: 10.1371/journal.pgen.1002840. Epub 2012 Jul 26.

PMID:
22911650
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

A domain-based model for predicting large and complex pseudoknotted structures.

Cao S, Chen SJ.

RNA Biol. 2012 Feb;9(2):200-11. doi: 10.4161/rna.18488. Epub 2012 Feb 1.

PMID:
22418848
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

A classification of bioinformatics algorithms from the viewpoint of maximizing expected accuracy (MEA).

Hamada M, Asai K.

J Comput Biol. 2012 May;19(5):532-49. doi: 10.1089/cmb.2011.0197. Epub 2012 Feb 7. Review.

PMID:
22313125
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

TurboKnot: rapid prediction of conserved RNA secondary structures including pseudoknots.

Seetin MG, Mathews DH.

Bioinformatics. 2012 Mar 15;28(6):792-8. doi: 10.1093/bioinformatics/bts044. Epub 2012 Jan 27.

PMID:
22285566
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Understanding the transcriptome through RNA structure.

Wan Y, Kertesz M, Spitale RC, Segal E, Chang HY.

Nat Rev Genet. 2011 Aug 18;12(9):641-55. doi: 10.1038/nrg3049. Review.

PMID:
21850044
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming.

Sato K, Kato Y, Hamada M, Akutsu T, Asai K.

Bioinformatics. 2011 Jul 1;27(13):i85-93. doi: 10.1093/bioinformatics/btr215.

PMID:
21685106
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

TT2NE: a novel algorithm to predict RNA secondary structures with pseudoknots.

Bon M, Orland H.

Nucleic Acids Res. 2011 Aug;39(14):e93. doi: 10.1093/nar/gkr240. Epub 2011 May 18.

PMID:
21593129
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

RNA secondary structure analysis using RNAstructure.

Mathews DH.

Curr Protoc Bioinformatics. 2006 Mar;Chapter 12:Unit 12.6. doi: 10.1002/0471250953.bi1206s13.

PMID:
18428759
[PubMed - indexed for MEDLINE]
Free PMC Article

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