Professor, Department of Plant Biology
Associate Dean
Ph.D. (1976) University of Wisconsin, Madison

Contact

malmberg@uga.edu
  • Elected Fellow, AAAS, 2008
  • Study in a Second Discipline Award, University of Georgia, 2001-2002
  • Outstanding Teaching Award, University of Georgia, 1991
  • Grant Support -
    • "The Evolution of Wthe Worldwide Leaf Economic Spectrum (WLES) in Helianthus," NSF
Selected Publications:
  • Srivastava, A., Zhang, X., LaMarca, S., Cai, L. and Malmberg, R.L. 2013. Patterns of chromatin-modifications discriminate different genomic features in Arabidopsis. International Journal of Bioinformatics Research and Applications, accepted.
  • Ding, L. Robertson, J., Malmberg, R.L. and Cai, L. 2013. Protein closed loop prediction from contact probabilities. International Journal of Bioinformatics Research and Applications, accepted
  • Manzour, A., Wang, Y.F., Shaw, T.I. and Malmberg, R.L. 2013. Information-theoretic uncertainty of scfg-modeled folding space of the non-coding RNA. Journal of Theoretical Biology 318: 140-163.
  • Zhang, D., Xue, X., Malmberg, R.L. and Cai, L. 2012. Trfolder-w: A web server for telomerase RNA structure prediction in yeast genomes. Bioinformatics 28: 2696-97.
  • Wang, Y.F., Manzour, A., Shareghi, P., Shaw, T.I., Li, Y.W., Malmberg, R.L. and Cai, L.M. 2012. Stable stem enabled shannon entropies distinguish non-coding RNAs from random backgrounds. BMC Bioinformatics 13.
  • Shareghi, P., Wang, Y.F., Malmberg, R. and Cai, L.M. 2012. Simultaneous prediction of RNA secondary structure and helix coaxial stacking. BMC Genomics 13.
  • Samis, K.E., Murren, C.J., Bossdorf, O., Donohue, K., Fenster, C.B., Malmberg R.L., Purugganan, M.D. and Stinchcombe, J.R. 2012. Longitudinal trends in climate drive flowering time clines in North American Arabidopsis thaliana. Ecology and Evolution 2: 1162-80.
  • Wang, Y., Manzour, A., Shareghi, P., Shaw, T., Li, Y., Malmberg, R.L. and Cai, L. 2011. Stable stem enabled shannon entropies distinguish ncRNA from random backgrounds. Proceedings of the International Conferences on Computational Advances in Bio and Medical Sciences: 184-89.
  • Srivastava, A., Rogers, W.L., Breton, C.M., Cai, L. and Malmberg, R.L. 2011. Transcriptome analysis of Sarracenia, an insectivorous plant. DNA Research 18: 253-61.
  • Srivastava, A., Cai, L., Mrazek, J. and Malmberg, R.L. 2011. Mutational patterns in RNA secondary structure evolution examined in three RNA families. PLoS One 6: e20484.
  • Shaw, T.I., Manzour, A., Wang, Y., Malmberg, R.L. and Cai, L. 2011. Analyzing modular RNA structure reveals low global structural entropy in microRNA sequences. Journal of Bioinformatics and Computational Biology 9: 283-298.
  • Guo, L., Zhang, D., Malmberg, R.L and Cai, L. 2011. Computational prediction of novel telomerase RNAs in yeast genomes. International Journal of Bioinformatics Research and Applications 7: 63-81.
  • Shaw, T.I., Manzour, A., Wang, Y., Malmberg, R.L. and Cai, L. 2010. Analyzing modular RNA structure though shannon entropy reveals low global structural entropy in miRNAs. CSB Conference Proceedings 9: 145-155.
  • Rogers, W.L., Cruse-Sanders, J.M., Determann, R. and Malmberg, R.L. 2010. Development and characterization of microsatellite markers in Sarracenia I. (pitcher plant) species. Conservation Genetics Resources 2: 75-79.
  • Malmberg, R.L., Shaw, T.I. and Cai, L. 2010. RNApasta: A computational tool for analysis of RNA alignments. International Journal of Bioinformatics Research and Applications 6: 571-83.
  • Huang, Z., Malmberg, R.L., Mohebbi, M. and Cai, L. 2010. RNAv: Non-coding RNA secondary structure variation search via graph homomorphism. CSB Conference Proceedings 9: 56-69.
  • Wang, Y.F., Huang, Z.B., Wu, Y., Malmberg, R.L. and Cai, L.M. 2009. RNAtops-w: A web server for RNA structure searches of genomes. Bioinformatics 25: 1081-81.
  • Zhao, J.Z., Malmberg, R.L. and Cai, L.M. 2008. Rapid ab initio prediciton of RNA pseudoknots via graph tree decomposition. Journal of Mathematical Biology 56: 145-149.
  • Momany, M., Pan, F. and Malmberg, R.L. 2008. Evolution and conserved domains of the septins. In The Septins, Hall, P., Russell, H. and Pringle, J., eds. (John Wiley and Sons): 35-5.
  • Huang, Z.B., Wu, Y., Robertson, J., Feng, L., Malmberg, R.L. and Cai, L.M. 2008. Fast and accurate search for non-coding RNA pseudoknot structures in genomes. Bioinformatics 24: 2281-87.
  • Pan, F.F., Malmberg, R.L. and Momany, M. 2007. Analysis of septins across kingdoms reveals ortholoyg and new motifs. BMC Evolutionary Biology 7: 103.
  • Brouillette, L.C., Rosenthal, D.M., REseberg, L.H., Lexer, C., Malmberg, R.L. and Donovan, L.A. 2007. Genetic architecture of leaf ecophysiological traits in helinathus. Journal of Heredity 98: 142-146.
  • Zhao, J.Z., Malmberg, R.L. and Cai, L.M. 2006. Rapid ab initio RNA folding including pseudoknots via graph tree decomposition. In Algorithms in Bioinformatics, proceedings: 262-273.
  • Zhao, J., Cai, L. and Malmberg, R.L. 2006. Learning the parameters of stochastic grammar models for RNA structures with pseudoknots. IEEE Xplore, Proceedings of the IEEE Conference on Granular Computing.
  • Song, Y.L., Lui, C.M., Malmberg, R.L. and Cai, L.M. 2006. Phylogenetic network interferences through efficient haplotyping. In Algorithms in Bioinformatics, proceedings: 68-79.
  • Song, Y., Lui, C., Malmberg, R.L., He, C., and Cai, L. 2006. Memory efficeint aligment between RNA sequences and stochastic grammar models of pseudoknots. International Journal of Bioinformations Research and Applications 2: 289-304.
  • Song, Y., Lui, C., Huang, X., Malmberg, R.L., Xu, Y. and Cai, L. 2006. Efficient parameterized algorithms for biopolymer structure-seqeunce alignment. IEEE-ACM Transactions ofn Computational Biology and Bioinformatics3: 423-432.
  • Lui, C., Song, Y., Hu, P., Malmberg, R.L. and Cai, L. 2006. Efficient annotation of non-coding RNA structures including pseudoknots via automated filters. IEEE CSB Proceedings.
  • Song, Y.L., Zhao, J.Z., Lui, C.M., Malmberg, R.L. and Cai, L.M. 2005. RNA structural homology search wth a succint stochastic grammar model. Journal of Computer Science and Technology 20: 454-464.
  • Song, Y., Lui, C.M., Huang, X.Z., Malmberg, R.L., Xu, Y. and Cai, L.M. 2005. Efficient parameterized algorithms for biopolymer structure-sequence alignment. In Algorithms in Bioinformaticcs, proceedings, Casadio, R. and Myers, G., eds.: 376-388.
  • Song, Y.L., Lui, C., Pan, F., Malmberg, R.L. and Cai, L. 2005. Tree decomposition based fast searching for RNA structures with and without pseudoknots. IEEE CSB Proceedings: 223-234.
  • Malmberg, R.L., Held, S., Waits, A. and Mauricio, R. 2005. Epistasis for fitness-related quantitative traits in Arabidopsis thaliana grown in the field and greenhouse. Genetics 171: 2013-2027.
  • Malmberg, R.L. and Mauricio, R. 2004. QTL-based evidence for the role of epistasis in evolution. Genetical Research 86: 89-95.
  • Song, Y., Zhao, J., Liu, K., Malmberg, R., and Cai, L. 2005. RNA structural homology search with a succinct grammar model. Journal of Computer Science and Technology 3692: 376-388.
  • Liu, C., Song, Y., Malmberg, R.L. and Cai, L. 2005. Profiling and searching for RNA pseudoknot structures in genomes. In Transactions on Computational Systems Biology II, Priaimi, C. and Zelikovsky, A., eds.: 37-47.
  • Liu, C., Song, Y., Malmberg, R.L. and Cai, L. 2005. Profiling and searching for RNA pseudoknot structures in genomes. In Computational Science - iccs 2005, part 2: 968-975.
  • Hummel, I., Bourdais, G., Gouesbet, G., CouĂ©e, I., Yu, W., Malmberg, R.L., and El Amrani, A. 2004. Differential gene epxression of arginine decarboxylase gene expression in Arabidopsis thaliana: Contribution of transcriptional regulation and involvement in seed germination, root development, leaf senescence and pollen formation. New Phytologist 163: 519-531.
  • Lawrence, C.J., Zmasek, C.M., Dawe, R.K. and Malmberg, R.L. . 2004. LumberJack: a heuristic tool for sequence alignment exploration and phylogenetic inference. Bioinformatics 20: 1977-1979.
  • Lawrence, C.J., Dawe, R.K., Christie, K.R., Cleveland, D.W., Dawson, S.C., Endow, S.A., Goldstein, L.S.B., Goodson, H.V., Hirokawa, N., Howard, J., Malmberg, R.L., McIntosh, J.R., Mitchison, T.J., Reddy, A.S.N., Saxton, W.M., Schliwa, M., Scholey, J.M., Vale, R.D., Walczak, C.E. and Wordeman, L. . 2004. A standardized kinesin nomenclature. Journal of Cell Biology 167: 19-22.
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