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Results: 1 to 20 of 88

1.

Information-theoretic uncertainty of SCFG-modeled folding space of the non-coding RNA.

Manzourolajdad A, Wang Y, Shaw TI, Malmberg RL.

J Theor Biol. 2013 Feb 7;318:140-63. doi: 10.1016/j.jtbi.2012.10.023. Epub 2012 Nov 14.

PMID:
23160142
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

TRFolder-W: a web server for telomerase RNA structure prediction in yeast genomes.

Zhang D, Xue X, Malmberg RL, Cai L.

Bioinformatics. 2012 Oct 15;28(20):2696-7. doi: 10.1093/bioinformatics/bts506. Epub 2012 Aug 24.

PMID:
22923293
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Longitudinal trends in climate drive flowering time clines in North American Arabidopsis thaliana.

Samis KE, Murren CJ, Bossdorf O, Donohue K, Fenster CB, Malmberg RL, Purugganan MD, Stinchcombe JR.

Ecol Evol. 2012 Jun;2(6):1162-80. doi: 10.1002/ece3.262.

PMID:
22833792
[PubMed]
Free PMC Article
4.

Simultaneous prediction of RNA secondary structure and helix coaxial stacking.

Shareghi P, Wang Y, Malmberg R, Cai L.

BMC Genomics. 2012 Jun 11;13 Suppl 3:S7. doi: 10.1186/1471-2164-13-S3-S7.

PMID:
22759616
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Stable stem enabled Shannon entropies distinguish non-coding RNAs from random backgrounds.

Wang Y, Manzour A, Shareghi P, Shaw TI, Li YW, Malmberg RL, Cai L.

BMC Bioinformatics. 2012 Apr 12;13 Suppl 5:S1. doi: 10.1186/1471-2105-13-S5-S1.

PMID:
22537005
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Mutational patterns in RNA secondary structure evolution examined in three RNA families.

Srivastava A, Cai L, Mrázek J, Malmberg RL.

PLoS One. 2011;6(6):e20484. doi: 10.1371/journal.pone.0020484. Epub 2011 Jun 17.

PMID:
21698102
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Transcriptome analysis of sarracenia, an insectivorous plant.

Srivastava A, Rogers WL, Breton CM, Cai L, Malmberg RL.

DNA Res. 2011 Aug;18(4):253-61. doi: 10.1093/dnares/dsr014. Epub 2011 Jun 15.

PMID:
21676972
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Analyzing modular RNA structure reveals low global structural entropy in microRNA sequence.

Shaw TI, Manzour A, Wang Y, Malmberg RL, Cai L.

J Bioinform Comput Biol. 2011 Apr;9(2):283-98.

PMID:
21523933
[PubMed - indexed for MEDLINE]
9.

TRFolder: computational prediction of novel telomerase RNA structures in yeast genomes.

Guo L, Zhang D, Wang Y, Malmberg RL, McEachern M, Cai L.

Int J Bioinform Res Appl. 2011;7(1):63-81.

PMID:
21441097
[PubMed - indexed for MEDLINE]
10.

RNApasta: a tool for analysis of RNA structural alignments.

Malmberg RL, Shaw TI, Cai L.

Int J Bioinform Res Appl. 2010;6(6):571-83.

PMID:
21354963
[PubMed - indexed for MEDLINE]
11.

Development and characterization of microsatellite markers in Sarracenia L. (pitcher plant) species.

Rogers WL, Cruse-Sanders JM, Determann R, Malmberg RL.

Conserv Genet Resour. 2010 Dec 1;2(1):75-79.

PMID:
21170168
[PubMed]
Free PMC Article
12.

RNATOPS-W: a web server for RNA structure searches of genomes.

Wang Y, Huang Z, Wu Y, Malmberg RL, Cai L.

Bioinformatics. 2009 Apr 15;25(8):1080-1. doi: 10.1093/bioinformatics/btp095. Epub 2009 Mar 5.

PMID:
19269988
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Fast and accurate search for non-coding RNA pseudoknot structures in genomes.

Huang Z, Wu Y, Robertson J, Feng L, Malmberg RL, Cai L.

Bioinformatics. 2008 Oct 15;24(20):2281-7. doi: 10.1093/bioinformatics/btn393. Epub 2008 Aug 7.

PMID:
18687694
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

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]
15.

Rapid ab initio prediction of RNA pseudoknots via graph tree decomposition.

Zhao J, Malmberg RL, Cai L.

J Math Biol. 2008 Jan;56(1-2):145-59. Epub 2007 Sep 29.

PMID:
17906862
[PubMed - indexed for MEDLINE]
16.

Analysis of septins across kingdoms reveals orthology and new motifs.

Pan F, Malmberg RL, Momany M.

BMC Evol Biol. 2007 Jul 1;7:103.

PMID:
17601340
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Efficient annotation of non-coding RNA structures including pseudoknots via automated filters.

Liu C, Song Y, Hu P, Malmberg RL, Cai L.

Comput Syst Bioinformatics Conf. 2006:99-110.

PMID:
17369629
[PubMed - indexed for MEDLINE]
Free Article
18.

Genetic architecture of leaf ecophysiological traits in Helianthus.

Brouillette LC, Rosenthal DM, Rieseberg LH, Lexer C, Malmberg RL, Donovan LA.

J Hered. 2007 Mar-Apr;98(2):142-6. Epub 2007 Jan 5.

PMID:
17208933
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Efficient parameterized algorithms for biopolymer structure-sequence alignment.

Song Y, Liu C, Huang X, Malmberg RL, Xu Y, Cai L.

IEEE/ACM Trans Comput Biol Bioinform. 2006 Oct-Dec;3(4):423-32.

PMID:
17085850
[PubMed - indexed for MEDLINE]
20.

Tree decomposition based fast search of RNA structures including pseudoknots in genomes.

Song Y, Liu C, Malmberg R, Pan F, Cai L.

Proc IEEE Comput Syst Bioinform Conf. 2005:223-34.

PMID:
16447980
[PubMed - indexed for MEDLINE]

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