Professor and Head of Plant Biology
Ph.D. (1976) University of Wisconsin

Phone: 706-542-1850
Email: russell@plantbio.uga.edu

Research in the Malmberg Lab

My current research interests are in the broad areas of bioinformatics and plant evolutionary genetics. Most of my bioinformatics work is a collaboration with Liming Cai of the Computer Science Department to develop methods of modeling and searching genomes for non-coding RNAs. Within the area of plant evolution my major interest is in the role that epistatic interactions play in evolution. I have an additional project to study the genetics of the insect-eating pitcher plants.

Lab Members

Awards

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Research Interests

Bioinformatics - noncoding RNAs: In the last 10 years, small non-coding RNAs have been found to have many functions in cells and organisms. There are speculations that there are as many non-coding RNA genes as there are genes that encode proteins. One bioinformatic challenge is that, without an open reading frame as a clue, it is difficult to find putative non-coding RNA genes in a DNA sequence. Comparing the same non-coding RNA between organisms, it is common for them to share the same secondary structure, but the primary sequence is frequently divergent. Thus, genome searching for non-coding RNA genes becomes a problem in scanning DNA sequences for regions that can fold up into a characteristic RNA secondary structure (left figure).
Our project is aimed at modeling noncoding RNA structures, and aligning RNA structures to genomes in order to find new instances of a given non-coding RNA gene family. Our methods can model the RNA structural motif of pseudoknots (right figure) as well as stem loops.
Current projects include algorithm development, graphical user interface development, and the application of our methods to certain families of RNAs. We have recently been studying telomerase RNAs, involved in the maintenance of eukaryotic chromosome ends, and the roX RNAs involved in dosage compensation in Drosophila. Please also visit Liming Cai's and my RNA Informatics group web page.
I have several other collaborative bioinformatics projects involving the study of the evolution of eukaryotic gene families.

Selected Publications

• Cai, L., R. L. Malmberg, and Y. Wu. 2003. Stochastic modeling of RNA pseudoknotted structures: a grammatical approach. Bioinformatics 19:i66-i73.
• Hummel, I., G. Bourdais, G. Gouesbet, I. Couee, R. L. Malmberg, and A. El Amrani. 2004. Differential gene expression of arginine decarboxylase ADC1 and ADC2 in Arabidopsis thaliana: characterization of transcriptional regulation during seed germination and seedling development. New Phytologist 163:519-531.
• Lawrence, C., R. Dawe, K. Christie, D. Cleveland, S. Dawson, S. Endow, L. Goldstein, H. Goodson, N. Hirokawa, J. Howard, R. Malmberg, J. McIntosh, H. Miki, T. Mitchison, Y. Okada, A. Reddy, W. Saxton, M. Schliwa, J. Scholey, R. Vale, C. Walczak, and L. Wordeman. 2004. A standardized kinesin nomenclature. Journal of Cell Biology 167:19-22.
• Lawrence, C., C. Zmasek, R. Dawe, and R. Malmberg. 2004. LumberJack: a heuristic tool for sequence alignment exploration and phylogenetic inference. Bioinformatics 20:1977-1979.
• Liu, C. M., Y. L. Song, R. L. Malmberg, and L. M. Cai. 2005. Profiling and searching for RNA pseudoknot structures in genomes. Pp. 37-47. Transactions on Computational Systems Biology Ii.
• Malmberg, R. L., and R. Mauricio. 2005. QTL-based evidence for the role of epistasis in evolution. Genetical Research 86:89-95.
• Malmberg, R. L., S. Held, A. Waits, and R. Mauricio. 2005. Epistasis for fitness-related quantitative traits in Arabidopsis thaliana grown in the field and in the greenhouse. Genetics 171:2013-27.
• Song, Y. L., J. Z. Zhao, C. M. Liu, K. Liu, R. Malmberg, and L. M. Cai. 2005. RNA structural homology search with a succinct stochastic grammar model. Journal of Computer Science and Technology 20:454-464.
• Song, Y., C. Liu, F. Pan, R. L. Malmberg, and L. Cai. 2005. Tree decomposition based fast searching for RNA structures with and without pseudoknots. IEEE CSB Proceedings 223-234.
• Song, Y., C. Liu, X. Huang, R. L. Malmberg, Y. Xu, and L. Cai. 2005. Efficient parameterized algorithm for biopolymer structural-sequence alignment. WABI 2005, Lecture Notes in Bioinformatics 3692:376-388.
• Song, Y., C. Liu, R. L. Malmberg, C. He, and L. Cai. 2006. Memory efficient alignment between RNA sequences and stochastic grammar models of pseudoknots. International Journal of Bioinformatics Research and Applications 2: 289-304.
• Song, Y., C. Liu, X. Huang, R. Malmberg, Y. Xu, and L. Cai. 2006. Efficient parameterized algorithms for biopolymer structure-sequence alignment. IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press.
• Zhao, J., L. Cai, and R. L. Malmberg. 2006. Learning the parameters of stochastic grammar models for RNA structures with pseudoknots. IEEE Xplore, Proceedings of the IEEE Conference on Granular Computing, in press.
• Liu, C., Song, Y., Hu, P., Malmberg, R.L., Cai, L. 2006. Efficient annotation of non-coding RNA structures including pseudoknots via automated filters. IEEE CSB Proceedings, in press.
• Song, Y., C. Liu, R. Malmberg, Y. Xu, and L. Cai. 2006. Phylogenetic inferences through efficient haplotyping. WABI 2006, Lecture Notes in Bioinformatics, in press.
• Zhao, J., Malmberg, R.L., Cai, L. 2006. Rapid ab initio RNA folding including pseudoknots via graph tree decomposition. WABI 2006, Lecture Notes in Bioinformatics, in press.
• Pan, F., Malmberg, R.L., Momany, M. 2006. Evolution of the septins: orthology across kingdoms and identification of new motifs, submitted