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Items: 1 to 20 of 94


UGbS-Flex, a novel bioinformatics pipeline for imputation-free SNP discovery in polyploids without a reference genome: finger millet as a case study.

Qi P, Gimode D, Saha D, Schröder S, Chakraborty D, Wang X, Dida MM, Malmberg RL, Devos KM.

BMC Plant Biol. 2018 Jun 15;18(1):117. doi: 10.1186/s12870-018-1316-3.


Development of Transcriptomic Markers for Population Analysis Using Restriction Site Associated RNA Sequencing (RARseq).

Alabady MS, Rogers WL, Malmberg RL.

PLoS One. 2015 Aug 4;10(8):e0134855. doi: 10.1371/journal.pone.0134855. eCollection 2015.


Species tree estimation of diploid Helianthus (Asteraceae) using target enrichment.

Stephens JD, Rogers WL, Mason CM, Donovan LA, Malmberg RL.

Am J Bot. 2015 Jun;102(6):910-20. doi: 10.3732/ajb.1500031. Epub 2015 Jun 18.


Accurate prediction of RNA nucleotide interactions with backbone k-tree model.

Ding L, Xue X, LaMarca S, Mohebbi M, Samad A, Malmberg RL, Cai L.

Bioinformatics. 2015 Aug 15;31(16):2660-7. doi: 10.1093/bioinformatics/btv210. Epub 2015 Apr 16.


Effect of reducing the paediatric stavudine dose by half: a physiologically-based pharmacokinetic model.

Sy SK, Malmberg R, Matsushima A, Asin-Prieto E, Rosenkranz B, Cotton MF, Derendorf H, Innes S.

Int J Antimicrob Agents. 2015 Apr;45(4):413-9. doi: 10.1016/j.ijantimicag.2014.12.016. Epub 2015 Jan 19.


Resolving phylogenetic relationships of the recently radiated carnivorous plant genus Sarracenia using target enrichment.

Stephens JD, Rogers WL, Heyduk K, Cruse-Sanders JM, Determann RO, Glenn TC, Malmberg RL.

Mol Phylogenet Evol. 2015 Apr;85:76-87. doi: 10.1016/j.ympev.2015.01.015. Epub 2015 Feb 14.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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