Display Settings:

Format
Items per page
Sort by

Send to:

Choose Destination

Results: 1 to 20 of 114

1.

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
2.

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
3.

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]
4.

Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints.

Dowell RD, Eddy SR.

BMC Bioinformatics. 2006 Sep 4;7:400.

PMID:
16952317
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

StatAlign 2.0: combining statistical alignment with RNA secondary structure prediction.

Arunapuram P, Edvardsson I, Golden M, Anderson JW, Novák A, Sükösd Z, Hein J.

Bioinformatics. 2013 Mar 1;29(5):654-5. doi: 10.1093/bioinformatics/btt025. Epub 2013 Jan 17.

PMID:
23335014
[PubMed - indexed for MEDLINE]
Free Article
6.

Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments.

Seemann SE, Gorodkin J, Backofen R.

Nucleic Acids Res. 2008 Nov;36(20):6355-62. doi: 10.1093/nar/gkn544. Epub 2008 Oct 4.

PMID:
18836192
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Stochastic modeling of RNA pseudoknotted structures: a grammatical approach.

Cai L, Malmberg RL, Wu Y.

Bioinformatics. 2003;19 Suppl 1:i66-73.

PMID:
12855439
[PubMed - indexed for MEDLINE]
Free Article
8.

RNA secondary structure prediction using stochastic context-free grammars and evolutionary history.

Knudsen B, Hein J.

Bioinformatics. 1999 Jun;15(6):446-54.

PMID:
10383470
[PubMed - indexed for MEDLINE]
Free Article
9.

Bayesian sampling of evolutionarily conserved RNA secondary structures with pseudoknots.

Doose G, Metzler D.

Bioinformatics. 2012 Sep 1;28(17):2242-8. doi: 10.1093/bioinformatics/bts369. Epub 2012 Jul 13.

PMID:
22796961
[PubMed - indexed for MEDLINE]
Free Article
10.

Pair hidden Markov models on tree structures.

Sakakibara Y.

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

PMID:
12855464
[PubMed - indexed for MEDLINE]
Free Article
11.
12.

CONTRAfold: RNA secondary structure prediction without physics-based models.

Do CB, Woods DA, Batzoglou S.

Bioinformatics. 2006 Jul 15;22(14):e90-8.

PMID:
16873527
[PubMed - indexed for MEDLINE]
Free Article
13.

Multithreaded comparative RNA secondary structure prediction using stochastic context-free grammars.

Sükösd Z, Knudsen B, Vaerum M, Kjems J, Andersen ES.

BMC Bioinformatics. 2011 Apr 18;12:103. doi: 10.1186/1471-2105-12-103.

PMID:
21501497
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

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.

PMID:
15784748
[PubMed - indexed for MEDLINE]
Free Article
15.

Incorporating phylogenetic-based covarying mutations into RNAalifold for RNA consensus structure prediction.

Ge P, Zhang S.

BMC Bioinformatics. 2013 Apr 27;14:142. doi: 10.1186/1471-2105-14-142.

PMID:
23621982
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Consensus folding of unaligned RNA sequences revisited.

Bafna V, Tang H, Zhang S.

J Comput Biol. 2006 Mar;13(2):283-95.

PMID:
16597240
[PubMed - indexed for MEDLINE]
17.

Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction.

Dowell RD, Eddy SR.

BMC Bioinformatics. 2004 Jun 4;5:71.

PMID:
15180907
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Consensus shapes: an alternative to the Sankoff algorithm for RNA consensus structure prediction.

Reeder J, Giegerich R.

Bioinformatics. 2005 Sep 1;21(17):3516-23. Epub 2005 Jul 14.

PMID:
16020472
[PubMed - indexed for MEDLINE]
Free Article
19.

Accelerated probabilistic inference of RNA structure evolution.

Holmes I.

BMC Bioinformatics. 2005 Mar 24;6:73.

PMID:
15790387
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

DAFS: simultaneous aligning and folding of RNA sequences via dual decomposition.

Sato K, Kato Y, Akutsu T, Asai K, Sakakibara Y.

Bioinformatics. 2012 Dec 15;28(24):3218-24. doi: 10.1093/bioinformatics/bts612. Epub 2012 Oct 11.

PMID:
23060618
[PubMed - indexed for MEDLINE]
Free Article

Display Settings:

Format
Items per page
Sort by

Send to:

Choose Destination

Supplemental Content

Write to the Help Desk