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Items: 1 to 20 of 151

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.

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.

3.

SHAPE-Seq 2.0: systematic optimization and extension of high-throughput chemical probing of RNA secondary structure with next generation sequencing.

Loughrey D, Watters KE, Settle AH, Lucks JB.

Nucleic Acids Res. 2014 Dec 1;42(21). doi: 10.1093/nar/gku909. Epub 2014 Oct 10.

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.

5.

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.

7.

Characterizing RNA structures in vitro and in vivo with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq).

Watters KE, Yu AM, Strobel EJ, Settle AH, Lucks JB.

Methods. 2016 Jul 1;103:34-48. doi: 10.1016/j.ymeth.2016.04.002. Epub 2016 Apr 12.

8.

Mapping RNA Structure In Vitro with SHAPE Chemistry and Next-Generation Sequencing (SHAPE-Seq).

Watters KE, Lucks JB.

Methods Mol Biol. 2016;1490:135-62. doi: 10.1007/978-1-4939-6433-8_9.

PMID:
27665597
9.

SHAPE Selection (SHAPES) enrich for RNA structure signal in SHAPE sequencing-based probing data.

Poulsen LD, Kielpinski LJ, Salama SR, Krogh A, Vinther J.

RNA. 2015 May;21(5):1042-52. doi: 10.1261/rna.047068.114. Epub 2015 Mar 24.

10.

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.

11.

Selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) for direct, versatile and accurate RNA structure analysis.

Smola MJ, Rice GM, Busan S, Siegfried NA, Weeks KM.

Nat Protoc. 2015 Nov;10(11):1643-69. doi: 10.1038/nprot.2015.103. Epub 2015 Oct 1.

12.

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
13.

RNA structure framework: automated transcriptome-wide reconstruction of RNA secondary structures from high-throughput structure probing data.

Incarnato D, Neri F, Anselmi F, Oliviero S.

Bioinformatics. 2016 Feb 1;32(3):459-61. doi: 10.1093/bioinformatics/btv571. Epub 2015 Oct 19.

14.

A graph theoretical approach for predicting common RNA secondary structure motifs including pseudoknots in unaligned sequences.

Ji Y, Xu X, Stormo GD.

Bioinformatics. 2004 Jul 10;20(10):1591-602. Epub 2004 Feb 12.

PMID:
14962926
15.

Reproducible Analysis of Sequencing-Based RNA Structure Probing Data with User-Friendly Tools.

Kielpinski LJ, Sidiropoulos N, Vinther J.

Methods Enzymol. 2015;558:153-80. doi: 10.1016/bs.mie.2015.01.014. Epub 2015 Mar 3.

PMID:
26068741
16.

A quantitative analysis of secondary RNA structure using domination based parameters on trees.

Haynes T, Knisley D, Seier E, Zou Y.

BMC Bioinformatics. 2006 Mar 3;7:108.

17.

RNA-Seq gene expression estimation with read mapping uncertainty.

Li B, Ruotti V, Stewart RM, Thomson JA, Dewey CN.

Bioinformatics. 2010 Feb 15;26(4):493-500. doi: 10.1093/bioinformatics/btp692. Epub 2009 Dec 18.

18.
19.

2D-RNA-coupling numbers: a new computational chemistry approach to link secondary structure topology with biological function.

González-Díaz H, Agüero-Chapin G, Varona J, Molina R, Delogu G, Santana L, Uriarte E, Podda G.

J Comput Chem. 2007 Apr 30;28(6):1049-56.

PMID:
17279496
20.

Ensemble-based RNA secondary structure characterization.

Crozier SP, Garner HR.

IEEE Eng Med Biol Mag. 2007 Jan-Feb;26(1):72-86. No abstract available.

PMID:
17278775

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