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Results: 1 to 20 of 89

Similar articles for PubMed (Select 23847102)

1.

Widespread purifying selection on RNA structure in mammals.

Smith MA, Gesell T, Stadler PF, Mattick JS.

Nucleic Acids Res. 2013 Sep;41(17):8220-36. doi: 10.1093/nar/gkt596. Epub 2013 Jul 11.

2.

The RNAz web server: prediction of thermodynamically stable and evolutionarily conserved RNA structures.

Gruber AR, Neuböck R, Hofacker IL, Washietl S.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W335-8. Epub 2007 Apr 22.

3.
4.

New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes.

Parker BJ, Moltke I, Roth A, Washietl S, Wen J, Kellis M, Breaker R, Pedersen JS.

Genome Res. 2011 Nov;21(11):1929-43. doi: 10.1101/gr.112516.110. Epub 2011 Oct 12.

5.

Detection of RNA structures in porcine EST data and related mammals.

Seemann SE, Gilchrist MJ, Hofacker IL, Stadler PF, Gorodkin J.

BMC Genomics. 2007 Sep 10;8:316.

6.

Dinucleotide controlled null models for comparative RNA gene prediction.

Gesell T, Washietl S.

BMC Bioinformatics. 2008 May 27;9:248. doi: 10.1186/1471-2105-9-248.

7.
8.

Fast and reliable prediction of noncoding RNAs.

Washietl S, Hofacker IL, Stadler PF.

Proc Natl Acad Sci U S A. 2005 Feb 15;102(7):2454-9. Epub 2005 Jan 21.

9.

Use of tiling array data and RNA secondary structure predictions to identify noncoding RNA genes.

Weile C, Gardner PP, Hedegaard MM, Vinther J.

BMC Genomics. 2007 Jul 23;8:244.

10.

Systematic analysis of genomic organization and structure of long non-coding RNAs in the human genome.

Sun J, Zhou M, Mao ZT, Hao DP, Wang ZZ, Li CX.

FEBS Lett. 2013 Apr 2;587(7):976-82. doi: 10.1016/j.febslet.2013.02.036. Epub 2013 Feb 27.

11.

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.

12.

Distribution and intensity of constraint in mammalian genomic sequence.

Cooper GM, Stone EA, Asimenos G; NISC Comparative Sequencing Program, Green ED, Batzoglou S, Sidow A.

Genome Res. 2005 Jul;15(7):901-13. Epub 2005 Jun 17.

13.

Structured RNAs in the ENCODE selected regions of the human genome.

Washietl S, Pedersen JS, Korbel JO, Stocsits C, Gruber AR, Hackermüller J, Hertel J, Lindemeyer M, Reiche K, Tanzer A, Ucla C, Wyss C, Antonarakis SE, Denoeud F, Lagarde J, Drenkow J, Kapranov P, Gingeras TR, Guigó R, Snyder M, Gerstein MB, Reymond A, Hofacker IL, Stadler PF.

Genome Res. 2007 Jun;17(6):852-64.

14.

Identifying structural noncoding RNAs using RNAz.

Washietl S, Hofacker IL.

Curr Protoc Bioinformatics. 2007 Sep;Chapter 12:Unit 12.7. doi: 10.1002/0471250953.bi1207s19.

PMID:
18428784
15.
16.

Automatic detection of conserved base pairing patterns in RNA virus genomes.

Hofacker IL, Stadler PF.

Comput Chem. 1999 Jun 15;23(3-4):401-14.

PMID:
10404627
17.

Prediction of structural noncoding RNAs with RNAz.

Washietl S.

Methods Mol Biol. 2007;395:503-26.

PMID:
17993695
18.

An algorithm for detecting homologues of known structured RNAs in genomes.

Le SY, Maizel JV Jr, Zhang K.

Proc IEEE Comput Syst Bioinform Conf. 2004:300-10.

PMID:
16448023
19.

Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions.

Torarinsson E, Yao Z, Wiklund ED, Bramsen JB, Hansen C, Kjems J, Tommerup N, Ruzzo WL, Gorodkin J.

Genome Res. 2008 Feb;18(2):242-51. Epub 2007 Dec 20.

20.

Hairpins in a Haystack: recognizing microRNA precursors in comparative genomics data.

Hertel J, Stadler PF.

Bioinformatics. 2006 Jul 15;22(14):e197-202.

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