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Items: 1 to 20 of 110

1.

Computational analysis of noncoding RNAs.

Washietl S, Will S, Hendrix DA, Goff LA, Rinn JL, Berger B, Kellis M.

Wiley Interdiscip Rev RNA. 2012 Nov-Dec;3(6):759-78. doi: 10.1002/wrna.1134. Epub 2012 Sep 18. Review.

2.

Sequence and structure analysis of noncoding RNAs.

Washietl S.

Methods Mol Biol. 2010;609:285-306. doi: 10.1007/978-1-60327-241-4_17. Review.

PMID:
20221926
3.

DeepBase: annotation and discovery of microRNAs and other noncoding RNAs from deep-sequencing data.

Yang JH, Qu LH.

Methods Mol Biol. 2012;822:233-48. doi: 10.1007/978-1-61779-427-8_16.

PMID:
22144203
4.

An Ariadne's thread to the identification and annotation of noncoding RNAs in eukaryotes.

Soldà G, Makunin IV, Sezerman OU, Corradin A, Corti G, Guffanti A.

Brief Bioinform. 2009 Sep;10(5):475-89. doi: 10.1093/bib/bbp022. Epub 2009 Apr 21. Review.

PMID:
19383843
5.

De novo discovery of structured ncRNA motifs in genomic sequences.

Ruzzo WL, Gorodkin J.

Methods Mol Biol. 2014;1097:303-18. doi: 10.1007/978-1-62703-709-9_15. Review.

PMID:
24639166
6.

Folding and finding RNA secondary structure.

Mathews DH, Moss WN, Turner DH.

Cold Spring Harb Perspect Biol. 2010 Dec;2(12):a003665. doi: 10.1101/cshperspect.a003665. Epub 2010 Aug 4. Review.

7.
8.

Progress and Current Challenges in Modeling Large RNAs.

Somarowthu S.

J Mol Biol. 2016 Feb 27;428(5 Pt A):736-47. doi: 10.1016/j.jmb.2015.11.011. Epub 2015 Nov 14. Review.

9.

Rfam 12.0: updates to the RNA families database.

Nawrocki EP, Burge SW, Bateman A, Daub J, Eberhardt RY, Eddy SR, Floden EW, Gardner PP, Jones TA, Tate J, Finn RD.

Nucleic Acids Res. 2015 Jan;43(Database issue):D130-7. doi: 10.1093/nar/gku1063. Epub 2014 Nov 11.

10.

Computational prediction of microRNA genes.

Hertel J, Langenberger D, Stadler PF.

Methods Mol Biol. 2014;1097:437-56. doi: 10.1007/978-1-62703-709-9_20. Review.

PMID:
24639171
11.

Genome-wide annotation of microRNA primary transcript structures reveals novel regulatory mechanisms.

Chang TC, Pertea M, Lee S, Salzberg SL, Mendell JT.

Genome Res. 2015 Sep;25(9):1401-9. doi: 10.1101/gr.193607.115.

12.

Computational methods in noncoding RNA research.

Machado-Lima A, del Portillo HA, Durham AM.

J Math Biol. 2008 Jan;56(1-2):15-49. Epub 2007 Sep 4. Review.

PMID:
17786447
13.

From structure prediction to genomic screens for novel non-coding RNAs.

Gorodkin J, Hofacker IL.

PLoS Comput Biol. 2011 Aug;7(8):e1002100. doi: 10.1371/journal.pcbi.1002100. Epub 2011 Aug 4. Review.

14.

Rfam: annotating families of non-coding RNA sequences.

Daub J, Eberhardt RY, Tate JG, Burge SW.

Methods Mol Biol. 2015;1269:349-63. doi: 10.1007/978-1-4939-2291-8_22.

PMID:
25577390
15.

A computational pipeline for high- throughput discovery of cis-regulatory noncoding RNA in prokaryotes.

Yao Z, Barrick J, Weinberg Z, Neph S, Breaker R, Tompa M, Ruzzo WL.

PLoS Comput Biol. 2007 Jul;3(7):e126.

16.

Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome.

Washietl S, Hofacker IL, Lukasser M, Hüttenhofer A, Stadler PF.

Nat Biotechnol. 2005 Nov;23(11):1383-90.

PMID:
16273071
17.

Analyzing modular RNA structure reveals low global structural entropy in microRNA sequence.

Shaw TI, Manzour A, Wang Y, Malmberg RL, Cai L.

J Bioinform Comput Biol. 2011 Apr;9(2):283-98.

PMID:
21523933
18.

Computational genomics of noncoding RNA genes.

Eddy SR.

Cell. 2002 Apr 19;109(2):137-40. Review.

19.

Rsite: a computational method to identify the functional sites of noncoding RNAs.

Zeng P, Li J, Ma W, Cui Q.

Sci Rep. 2015 Mar 17;5:9179. doi: 10.1038/srep09179.

20.

Structure-based whole-genome realignment reveals many novel noncoding RNAs.

Will S, Yu M, Berger B.

Genome Res. 2013 Jun;23(6):1018-27. doi: 10.1101/gr.137091.111. Epub 2013 Jan 7.

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