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Items: 1 to 20 of 307

1.

Evolutionary triplet models of structured RNA.

Bradley RK, Holmes I.

PLoS Comput Biol. 2009 Aug;5(8):e1000483. doi: 10.1371/journal.pcbi.1000483. Epub 2009 Aug 28.

2.

Bayesian coestimation of phylogeny and sequence alignment.

Lunter G, Miklós I, Drummond A, Jensen JL, Hein J.

BMC Bioinformatics. 2005 Apr 1;6:83.

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Probabilistic phylogenetic inference with insertions and deletions.

Rivas E, Eddy SR.

PLoS Comput Biol. 2008 Sep 19;4(9):e1000172. doi: 10.1371/journal.pcbi.1000172.

6.

Accurate reconstruction of insertion-deletion histories by statistical phylogenetics.

Westesson O, Lunter G, Paten B, Holmes I.

PLoS One. 2012;7(4):e34572. doi: 10.1371/journal.pone.0034572. Epub 2012 Apr 20.

7.

STRAL: progressive alignment of non-coding RNA using base pairing probability vectors in quadratic time.

Dalli D, Wilm A, Mainz I, Steger G.

Bioinformatics. 2006 Jul 1;22(13):1593-9. Epub 2006 Apr 13.

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Fast online and index-based algorithms for approximate search of RNA sequence-structure patterns.

Meyer F, Kurtz S, Beckstette M.

BMC Bioinformatics. 2013 Jul 17;14:226. doi: 10.1186/1471-2105-14-226.

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
11.

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

Matsui H, Sato K, Sakakibara Y.

Bioinformatics. 2005 Jun 1;21(11):2611-7. Epub 2005 Mar 22.

13.

Vestige: maximum likelihood phylogenetic footprinting.

Wakefield MJ, Maxwell P, Huttley GA.

BMC Bioinformatics. 2005 May 29;6:130.

14.

Noncoding RNA gene detection using comparative sequence analysis.

Rivas E, Eddy SR.

BMC Bioinformatics. 2001;2:8. Epub 2001 Oct 10.

15.

Pair hidden Markov models on tree structures.

Sakakibara Y.

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

16.

Reconstructing ancestral genomic sequences by co-evolution: formal definitions, computational issues, and biological examples.

Tuller T, Birin H, Kupiec M, Ruppin E.

J Comput Biol. 2010 Sep;17(9):1327-44. doi: 10.1089/cmb.2010.0112.

PMID:
20874411
17.

RNA structural alignments, part I: Sankoff-based approaches for structural alignments.

Havgaard JH, Gorodkin J.

Methods Mol Biol. 2014;1097:275-90. doi: 10.1007/978-1-62703-709-9_13.

PMID:
24639164
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19.

RNA structural alignments, part II: non-Sankoff approaches for structural alignments.

Asai K, Hamada M.

Methods Mol Biol. 2014;1097:291-301. doi: 10.1007/978-1-62703-709-9_14.

PMID:
24639165
20.

Using evolutionary Expectation Maximization to estimate indel rates.

Holmes I.

Bioinformatics. 2005 May 15;21(10):2294-300. Epub 2005 Feb 24.

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