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Results: 1 to 20 of 228

1.

Stem kernels for RNA sequence analyses.

Sakakibara Y, Popendorf K, Ogawa N, Asai K, Sato K.

J Bioinform Comput Biol. 2007 Oct;5(5):1103-22.

PMID:
17933013
[PubMed - indexed for MEDLINE]
2.

Genome-wide searching with base-pairing kernel functions for noncoding RNAs: computational and expression analysis of snoRNA families in Caenorhabditis elegans.

Morita K, Saito Y, Sato K, Oka K, Hotta K, Sakakibara Y.

Nucleic Acids Res. 2009 Feb;37(3):999-1009. doi: 10.1093/nar/gkn1054. Epub 2009 Jan 7.

PMID:
19129214
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Marginalized kernels for RNA sequence data analysis.

Kin T, Tsuda K, Asai K.

Genome Inform. 2002;13:112-22.

PMID:
14571380
[PubMed - indexed for MEDLINE]
4.

Directed acyclic graph kernels for structural RNA analysis.

Sato K, Mituyama T, Asai K, Sakakibara Y.

BMC Bioinformatics. 2008 Jul 22;9:318. doi: 10.1186/1471-2105-9-318.

PMID:
18647390
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Memory efficient alignment between RNA sequences and stochastic grammar models of pseudoknots.

Song Y, Liu C, Malmberg RL, He C, Cai L.

Int J Bioinform Res Appl. 2006;2(3):289-304.

PMID:
18048167
[PubMed - indexed for MEDLINE]
6.

Computational analysis of RNAs.

Eddy SR.

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

PMID:
17381287
[PubMed - indexed for MEDLINE]
7.

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
[PubMed - indexed for MEDLINE]
Free Article
8.

Stochastic context-free grammars for tRNA modeling.

Sakakibara Y, Brown M, Hughey R, Mian IS, Sjölander K, Underwood RC, Haussler D.

Nucleic Acids Res. 1994 Nov 25;22(23):5112-20.

PMID:
7800507
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Pair hidden Markov models on tree structures.

Sakakibara Y.

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

PMID:
12855464
[PubMed - indexed for MEDLINE]
Free Article
10.

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]
11.

Prediction of RNA secondary structure with pseudoknots using integer programming.

Poolsap U, Kato Y, Akutsu T.

BMC Bioinformatics. 2009 Jan 30;10 Suppl 1:S38. doi: 10.1186/1471-2105-10-S1-S38.

PMID:
19208139
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Pfold: RNA secondary structure prediction using stochastic context-free grammars.

Knudsen B, Hein J.

Nucleic Acids Res. 2003 Jul 1;31(13):3423-8.

PMID:
12824339
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Evolutionary rate variation and RNA secondary structure prediction.

Knudsen B, Andersen ES, Damgaard C, Kjems J, Gorodkin J.

Comput Biol Chem. 2004 Jul;28(3):219-26.

PMID:
15261152
[PubMed - indexed for MEDLINE]
14.

A mini-greedy algorithm for faster structural RNA stem-loop search.

Gorodkin J, Lyngso RB, Stormo GD.

Genome Inform. 2001;12:184-93.

PMID:
11791237
[PubMed - indexed for MEDLINE]
15.

An algorithm for searching RNA motifs in genomic sequences.

Liu J, Ma B, Zhang K.

Biomol Eng. 2007 Sep;24(3):343-50. Epub 2007 Mar 3.

PMID:
17482512
[PubMed - indexed for MEDLINE]
16.

Learned random-walk kernels and empirical-map kernels for protein sequence classification.

Min R, Bonner A, Li J, Zhang Z.

J Comput Biol. 2009 Mar;16(3):457-74. doi: 10.1089/cmb.2008.0031.

PMID:
19254184
[PubMed - indexed for MEDLINE]
17.

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]
18.

Automatic RNA secondary structure determination with stochastic context-free grammars.

Grate L.

Proc Int Conf Intell Syst Mol Biol. 1995;3:136-44.

PMID:
7584430
[PubMed - indexed for MEDLINE]
19.

GPRM: A genetic programming approach to finding common RNA secondary structure elements.

Hu YJ.

Nucleic Acids Res. 2003 Jul 1;31(13):3446-9.

PMID:
12824343
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

RNA secondary structural alignment with conditional random fields.

Sato K, Sakakibara Y.

Bioinformatics. 2005 Sep 1;21 Suppl 2:ii237-42.

PMID:
16204111
[PubMed - indexed for MEDLINE]
Free Article

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