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Results: 18

1.

SCFGs in RNA secondary structure prediction RNA secondary structure prediction: a hands-on approach.

Sükösd Z, Andersen ES, Lyngsø R.

Methods Mol Biol. 2014;1097:143-62. doi: 10.1007/978-1-62703-709-9_8.

PMID:
24639159
[PubMed - in process]
2.

Oxfold: kinetic folding of RNA using stochastic context-free grammars and evolutionary information.

Anderson JW, Haas PA, Mathieson LA, Volynkin V, Lyngsø R, Tataru P, Hein J.

Bioinformatics. 2013 Mar 15;29(6):704-10. doi: 10.1093/bioinformatics/btt050. Epub 2013 Feb 8.

PMID:
23396120
[PubMed - indexed for MEDLINE]
Free Article
3.

Frnakenstein: multiple target inverse RNA folding.

Lyngsø RB, Anderson JW, Sizikova E, Badugu A, Hyland T, Hein J.

BMC Bioinformatics. 2012 Oct 9;13:260. doi: 10.1186/1471-2105-13-260.

PMID:
23043260
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Evolving stochastic context--free grammars for RNA secondary structure prediction.

Wj Anderson J, Tataru P, Staines J, Hein J, Lyngsø R.

BMC Bioinformatics. 2012 May 4;13:78. doi: 10.1186/1471-2105-13-78.

PMID:
22559985
[PubMed - in process]
Free PMC Article
5.

Reconstructing the ancestral germ line methylation state of young repeats.

Feuerbach L, Lyngsø RB, Lengauer T, Hein J.

Mol Biol Evol. 2011 Jun;28(6):1777-84. doi: 10.1093/molbev/msr001. Epub 2011 Jan 6.

PMID:
21212152
[PubMed - indexed for MEDLINE]
Free Article
6.

Dynamics based alignment of proteins: an alternative approach to quantify dynamic similarity.

Münz M, Lyngsø R, Hein J, Biggin PC.

BMC Bioinformatics. 2010 Apr 14;11:188. doi: 10.1186/1471-2105-11-188.

PMID:
20398246
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC.

Satija R, Novák A, Miklós I, Lyngsø R, Hein J.

BMC Evol Biol. 2009 Aug 28;9:217. doi: 10.1186/1471-2148-9-217.

PMID:
19715598
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Stochastic models of sequence evolution including insertion-deletion events.

Miklós I, Novák A, Satija R, Lyngsø R, Hein J.

Stat Methods Med Res. 2009 Oct;18(5):453-85. doi: 10.1177/0962280208099500. Epub 2009 Feb 16.

PMID:
19221170
[PubMed - indexed for MEDLINE]
9.

An analysis of structural influences on selection in RNA genes.

Mimouni NK, Lyngsø RB, Griffiths-Jones S, Hein J.

Mol Biol Evol. 2009 Jan;26(1):209-16. doi: 10.1093/molbev/msn240. Epub 2008 Oct 22.

PMID:
18948299
[PubMed - indexed for MEDLINE]
Free Article
10.

StatAlign: an extendable software package for joint Bayesian estimation of alignments and evolutionary trees.

Novák A, Miklós I, Lyngsø R, Hein J.

Bioinformatics. 2008 Oct 15;24(20):2403-4. doi: 10.1093/bioinformatics/btn457. Epub 2008 Aug 27.

PMID:
18753153
[PubMed - indexed for MEDLINE]
Free Article
11.

On recombination-induced multiple and simultaneous coalescent events.

Davies JL, Simancík F, Lyngsø R, Mailund T, Hein J.

Genetics. 2007 Dec;177(4):2151-60. Epub 2007 Oct 18.

PMID:
17947442
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Counting all possible ancestral configurations of sample sequences in population genetics.

Song YS, Lyngsø R, Hein J.

IEEE/ACM Trans Comput Biol Bioinform. 2006 Jul-Sep;3(3):239-51.

PMID:
17048462
[PubMed - indexed for MEDLINE]
13.

The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search.

Havgaard JH, Lyngsø RB, Gorodkin J.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W650-3.

PMID:
15980555
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%.

Havgaard JH, Lyngsø RB, Stormo GD, Gorodkin J.

Bioinformatics. 2005 May 1;21(9):1815-24. Epub 2005 Jan 18.

PMID:
15657094
[PubMed - indexed for MEDLINE]
Free Article
15.

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]
16.

RNA pseudoknot prediction in energy-based models.

Lyngsø RB, Pedersen CN.

J Comput Biol. 2000;7(3-4):409-27.

PMID:
11108471
[PubMed - indexed for MEDLINE]
17.

Metrics and similarity measures for hidden Markov models.

Lyngsø RB, Pedersen CN, Nielsen H.

Proc Int Conf Intell Syst Mol Biol. 1999:178-86.

PMID:
10786300
[PubMed - indexed for MEDLINE]
18.

Fast evaluation of internal loops in RNA secondary structure prediction.

Lyngsø RB, Zuker M, Pedersen CN.

Bioinformatics. 1999 Jun;15(6):440-5.

PMID:
10383469
[PubMed - indexed for MEDLINE]
Free Article

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