Malmberg Research

Russell L. Malmberg
Professor of Plant Biology, also Appointed in Genetics
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Bioinformatics and Evolutionary Genetics
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.
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.
Genetics of Pitcher Plant Morphology:
Pitcher plants trap insects as a dietary supplement. Most of North America has a single pitcher plant species, Sarracenia purpurea, while the southeastern U.S. is home to 7 additional species, each with different pitcher morphologies. An additional complication is that hybrids frequently form between these species. We have generated F2 offspring from crosses between different Sarracenia species, and are studying the inheritance of pitcher morphology. It is possible to determine the insects that have entered the pitchers since their chitin is not digested. Hence, we can study the genetics of insect predation preference in the same F2 plants. The picture on the left is of a hybrid plant showing features of both parents, Sarracenia purpurea and Sarracenia psitticina. On the right is a photograph of a wall mural painted in the Malmberg lab by botanical illustrator Christie Newman.
Genetic Epistasis in Evolution:
One of the basic, controversial, questions in evolutionary biology is the extent to which genetic epistasis plays a role in local adaptations of populations, and in the process of speciation. By an analysis of recombinant inbred lines of Arabidopsis thaliana, grown in the field, we have demonstrated that epistatic interactions are more important than additive traits for fitness in these lines. The (left) figure shows the genetic map locations of the additive and epistatic QTLs for fruit number in these lines. The green lines connect interacting loci. Some loci may be participating in more than one interaction, and some have both additive and epistatic effects. Current experiments include a detailed genetic analysis of the epistatic interactions we have found, testing the network of interactions shown in the figure. We have also identified local populations of Arabidopsis thaliana that are well adapted to the growth conditions in northeast Georgia (right figure). We are using these populations to examine the genetic basis of local adaptations; see our Arabidopsis patch pictures.
Selected Recent 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. Zhao, J., Malmberg, R.L., Cai, L. 2006. Rapid ab initio RNA folding including pseudoknots via graph tree decomposition. WABI 2006, Computer Science 4175: 262-273. Song, Y., C. Liu, R. Malmberg, Y. Xu, and L. Cai. 2006. Phylogenetic inferences through efficient haplotyping. WABI 2006, Lecture Notes in Bioinformatics 4175:68-79 Song, Y., C. Liu, X. Huang, R. Malmberg, Y. Xu, and L. Cai. 2006. Efficient biopolymer structure-sequence alignment. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 3: 423-432. 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 170-175. 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 99-110. Brouillette, L.C., Rosenthal, D.M., Rieseberg, L.H., Lexer, C., Malmberg, R.L., Donovan, L.A. 2007. Genetic architecture of leaf ecophysiological traits in Helianthus. Journal of Heredity 98: 142-146. Pan, F., R. L. Malmberg, M. Momany. 2007. Evolution of the septins: orthology across kingdoms and identification of new motifs. BMC Evolutionary Biology 7:103. Zhao, J., R.L. Malmberg, L. Cai. 2007. Rapid ab initio RNA pseudoknot prediction via graph tree decomposition, Journal of Mathematical Biology, in press Momany, M., F. Pan, R.L. Malmberg. 2007. Evolution and conserved domains of the septins, submitted. Pan, F., D. Che, M. Momany, L. Cai, R.L. Malmberg. 2007. Protein Co-evolution and Its Applications in Residue Contact Prediction, submitted
Grant Support:
Searching Genomes for Non-Coding RNAs by Their Structure. Liming Cai, Russell Malmberg, Michael McEachern. NIH BISTI Genetic Analysis of Pitcher Morphology and Insectivory in Sarracenia, submitted.

Bioinformatics and Evolutionary Genetics

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.

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.

Genetics of Pitcher Plant Morphology:

Pitcher plants trap insects as a dietary supplement. Most of North America has a single pitcher plant species, Sarracenia purpurea, while the southeastern U.S. is home to 7 additional species, each with different pitcher morphologies. An additional complication is that hybrids frequently form between these species. We have generated F2 offspring from crosses between different Sarracenia species, and are studying the inheritance of pitcher morphology. It is possible to determine the insects that have entered the pitchers since their chitin is not digested. Hence, we can study the genetics of insect predation preference in the same F2 plants. The picture on the left is of a hybrid plant showing features of both parents, Sarracenia purpurea and Sarracenia psitticina.
On the right is a photograph of a wall mural painted in the Malmberg lab by botanical illustrator Christie Newman.

Genetic Epistasis in Evolution:

One of the basic, controversial, questions in evolutionary biology is the extent to which genetic epistasis plays a role in local adaptations of populations, and in the process of speciation. By an analysis of recombinant inbred lines of Arabidopsis thaliana, grown in the field, we have demonstrated that epistatic interactions are more important than additive traits for fitness in these lines.

The (left) figure shows the genetic map locations of the additive and epistatic QTLs for fruit number in these lines. The green lines connect interacting loci. Some loci may be participating in more than one interaction, and some have both additive and epistatic effects. Current experiments include a detailed genetic analysis of the epistatic interactions we have found, testing the network of interactions shown in the figure.
We have also identified local populations of Arabidopsis thaliana that are well adapted to the growth conditions in northeast Georgia (right figure). We are using these populations to examine the genetic basis of local adaptations; see our Arabidopsis patch pictures.

Selected Recent 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.
Zhao, J., Malmberg, R.L., Cai, L. 2006. Rapid ab initio RNA folding including pseudoknots via graph tree decomposition. WABI 2006, Computer Science 4175: 262-273.
Song, Y., C. Liu, R. Malmberg, Y. Xu, and L. Cai. 2006. Phylogenetic inferences through efficient haplotyping. WABI 2006, Lecture Notes in Bioinformatics 4175:68-79
Song, Y., C. Liu, X. Huang, R. Malmberg, Y. Xu, and L. Cai. 2006. Efficient biopolymer structure-sequence alignment. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 3: 423-432.
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 170-175.
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 99-110.
Brouillette, L.C., Rosenthal, D.M., Rieseberg, L.H., Lexer, C., Malmberg, R.L., Donovan, L.A. 2007. Genetic architecture of leaf ecophysiological traits in Helianthus. Journal of Heredity 98: 142-146.
Pan, F., R. L. Malmberg, M. Momany. 2007. Evolution of the septins: orthology across kingdoms and identification of new motifs. BMC Evolutionary Biology 7:103.
Zhao, J., R.L. Malmberg, L. Cai. 2007. Rapid ab initio RNA pseudoknot prediction via graph tree decomposition, Journal of Mathematical Biology, in press
Momany, M., F. Pan, R.L. Malmberg. 2007. Evolution and conserved domains of the septins, submitted.
Pan, F., D. Che, M. Momany, L. Cai, R.L. Malmberg. 2007. Protein Co-evolution and Its Applications in Residue Contact Prediction, submitted

Grant Support:

Searching Genomes for Non-Coding RNAs by Their Structure. Liming Cai, Russell Malmberg, Michael McEachern. NIH BISTI
Genetic Analysis of Pitcher Morphology and Insectivory in Sarracenia, submitted.

RNA Informatics Group:	Malmberg Lab:
Dongsheng Che, Graduate Student. Liang Feng, Graduate Student. Leilei Guo, Graduate Student. Zhibin Huang, Graduate Student. Jonathan Myers, Graduate Student. Fangfang Pan, Graduate Student. Joseph Robertson, Graduate Student. Yong Wu, Graduate Student. Chi Xie, Graduate Student. Dong Zhang, Graduate Student. Liming Cai, Computer Science Faculty.	Joanne Davis, Technician. Liang Feng, Graduate Student. Fangfang Pan, Graduate Student. Will Rogers, Technician.

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