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Results: 1 to 20 of 117

1.

Modeling and automation of sequencing-based characterization of RNA structure.

Aviran S, Trapnell C, Lucks JB, Mortimer SA, Luo S, Schroth GP, Doudna JA, Arkin AP, Pachter L.

Proc Natl Acad Sci U S A. 2011 Jul 5;108(27):11069-74. doi: 10.1073/pnas.1106541108. Epub 2011 Jun 3.

PMID:
21642536
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq).

Lucks JB, Mortimer SA, Trapnell C, Luo S, Aviran S, Schroth GP, Pachter L, Doudna JA, Arkin AP.

Proc Natl Acad Sci U S A. 2011 Jul 5;108(27):11063-8. doi: 10.1073/pnas.1106501108. Epub 2011 Jun 3.

PMID:
21642531
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

RNA structure probing dash seq.

Weeks KM.

Proc Natl Acad Sci U S A. 2011 Jul 5;108(27):10933-4. doi: 10.1073/pnas.1107835108. Epub 2011 Jun 23. No abstract available.

PMID:
21700884
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Quantitative dimethyl sulfate mapping for automated RNA secondary structure inference.

Cordero P, Kladwang W, VanLang CC, Das R.

Biochemistry. 2012 Sep 11;51(36):7037-9. Epub 2012 Aug 29.

PMID:
22913637
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolution.

Wilkinson KA, Merino EJ, Weeks KM.

Nat Protoc. 2006;1(3):1610-6.

PMID:
17406453
[PubMed - indexed for MEDLINE]
6.

STR2: a structure to string approach for locating G-box riboswitch shapes in pre-selected genes.

Bergig O, Barash D, Nudler E, Kedem K.

In Silico Biol. 2004;4(4):593-604.

PMID:
15752075
[PubMed - indexed for MEDLINE]
7.

ShapeFinder: a software system for high-throughput quantitative analysis of nucleic acid reactivity information resolved by capillary electrophoresis.

Vasa SM, Guex N, Wilkinson KA, Weeks KM, Giddings MC.

RNA. 2008 Oct;14(10):1979-90. doi: 10.1261/rna.1166808. Epub 2008 Sep 4.

PMID:
18772246
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

CONTRAfold: RNA secondary structure prediction without physics-based models.

Do CB, Woods DA, Batzoglou S.

Bioinformatics. 2006 Jul 15;22(14):e90-8.

PMID:
16873527
[PubMed - indexed for MEDLINE]
Free Article
9.

Computational analysis of RNAs.

Eddy SR.

Cold Spring Harb Symp Quant Biol. 2006;71:117-28.

PMID:
17381287
[PubMed - indexed for MEDLINE]
10.

Pair hidden Markov models on tree structures.

Sakakibara Y.

Bioinformatics. 2003;19 Suppl 1:i232-40.

PMID:
12855464
[PubMed - indexed for MEDLINE]
Free Article
11.

SeqFold: genome-scale reconstruction of RNA secondary structure integrating high-throughput sequencing data.

Ouyang Z, Snyder MP, Chang HY.

Genome Res. 2013 Feb;23(2):377-87. doi: 10.1101/gr.138545.112. Epub 2012 Oct 11.

PMID:
23064747
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Pair stochastic tree adjoining grammars for aligning and predicting pseudoknot RNA structures.

Matsui H, Sato K, Sakakibara Y.

Proc IEEE Comput Syst Bioinform Conf. 2004:290-9.

PMID:
16448022
[PubMed - indexed for MEDLINE]
13.

Statistical inferences for isoform expression in RNA-Seq.

Jiang H, Wong WH.

Bioinformatics. 2009 Apr 15;25(8):1026-32. doi: 10.1093/bioinformatics/btp113. Epub 2009 Feb 25.

PMID:
19244387
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Understanding the errors of SHAPE-directed RNA structure modeling.

Kladwang W, VanLang CC, Cordero P, Das R.

Biochemistry. 2011 Sep 20;50(37):8049-56. doi: 10.1021/bi200524n. Epub 2011 Aug 25.

PMID:
21842868
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Massive parallel-sequencing-based hydroxyl radical probing of RNA accessibility.

Kielpinski LJ, Vinther J.

Nucleic Acids Res. 2014 Apr;42(8):e70. doi: 10.1093/nar/gku167. Epub 2014 Feb 24.

PMID:
24569351
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

A general edit distance between RNA structures.

Jiang T, Lin G, Ma B, Zhang K.

J Comput Biol. 2002;9(2):371-88.

PMID:
12015887
[PubMed - indexed for MEDLINE]
17.

RNACompress: Grammar-based compression and informational complexity measurement of RNA secondary structure.

Liu Q, Yang Y, Chen C, Bu J, Zhang Y, Ye X.

BMC Bioinformatics. 2008 Mar 31;9:176. doi: 10.1186/1471-2105-9-176.

PMID:
18373878
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Probing the structure of RNAIII, the Staphylococcus aureus agr regulatory RNA, and identification of the RNA domain involved in repression of protein A expression.

Benito Y, Kolb FA, Romby P, Lina G, Etienne J, Vandenesch F.

RNA. 2000 May;6(5):668-79.

PMID:
10836788
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

RNA SHAPE analysis in living cells.

Spitale RC, Crisalli P, Flynn RA, Torre EA, Kool ET, Chang HY.

Nat Chem Biol. 2013 Jan;9(1):18-20. doi: 10.1038/nchembio.1131. Epub 2012 Nov 25.

PMID:
23178934
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Correlating SHAPE signatures with three-dimensional RNA structures.

Bindewald E, Wendeler M, Legiewicz M, Bona MK, Wang Y, Pritt MJ, Le Grice SF, Shapiro BA.

RNA. 2011 Sep;17(9):1688-96. doi: 10.1261/rna.2640111. Epub 2011 Jul 13.

PMID:
21752927
[PubMed - indexed for MEDLINE]
Free PMC Article
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