Index

My current research interests are in the broad areas of bioinformatics and plant evolutionary/ecological genetics. Will Rogers (left) and I are studying the genetics, evolution, and ecology, of the insect-eating pitcher plants (Sarracenia species). Most of my bioinformatics work is a collaboration with Liming Cai (right) of the Computer Science Department to develop methods of modeling and searching genomes for non-coding RNAs. See our RNA-Informatics web site.

Recent Publications:
Malmberg, R. L., L. Cai. 2009. RNApasta, A Computational Tool for Analysis of RNA Alignments, submitted Guo, L., D. Zhang, R. L. Malmberg, L. Cai. 2009. Computational Prediction of Novel Telomerase RNAs in Yeast Genomes, BMC Bioinformatics, submitted Wang, Y., Z. Huang, Z., Y. Wong, R.L. Malmberg, L. Cai. 2009. RNATOPS-W: A Web Server for RNA Structure Searches of Genomes. Bioinformatics, In press. doi:10.1093/bioinformatics/btp095 Momany, M., Pan, F. and R. Malmberg. 2008. Evolution and conserved domains of the septins. In The Septins (eds. P. Hall, H. Russell and J. Pringle), John Wiley and Sons Ltd., pages 35-45. Huang, Z., Y. Wu, J. Robertson, L. Feng, R.L. Malmberg, L. Cai. 2008. Searching for non-coding RNA pseudoknot structures in genomes via graph tree decomposition. Bioinformatics, 24: 2281-2287 Zhao, J., R.L. Malmberg, L. Cai. 2008. Rapid ab initio RNA pseudoknot prediction via graph tree decomposition. Journal of Mathematical Biology, 56: 145-159 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. 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. 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. 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. 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. 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 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. 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. 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, 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. Liu, C. M., Y. L. Song, R. L. Malmberg, and L. M. Cai. 2005. Profiling and searching for RNA pseudoknot structures in genomes. Proceedings of International Workshop in Bioinformatics Research and Applications (IWBRA 2005). Lecture Notes in Computer Science 3515: 968-975. 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. 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. Malmberg, R. L., and R. Mauricio. 2005. QTL-based evidence for the role of epistasis in evolution. Genetical Research 86:89-95. 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. 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. 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. 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. Malmberg, R. L. 2003. Plant mutagenesis and mutant screening Nature Encyclopedia of Life Sciences. London: Nature Publishing Group. Cai, L., R. L. Malmberg, and Y. Wu. 2003. Stochastic modeling of RNA pseudoknotted structures: a grammatical approach. Bioinformatics 19:i66-i73. Lawrence, C. J., R. L. Malmberg, M. G. Muszynski, and R. K. Dawe. 2002. Maximum likelihood methods reveal conservation of function among closely related kinesin families. Journal Of Molecular Evolution 54:42-53. Malmberg, R. L., and J. Godwin. 2001. Replacement of an old HPLC integrator with an inexpensive computer and custom software. Biotechniques 30:1306-1308.

Recent Publications:

Malmberg, R. L., L. Cai. 2009. RNApasta, A Computational Tool for Analysis of RNA Alignments, submitted
Guo, L., D. Zhang, R. L. Malmberg, L. Cai. 2009. Computational Prediction of Novel Telomerase RNAs in Yeast Genomes, BMC Bioinformatics, submitted
Wang, Y., Z. Huang, Z., Y. Wong, R.L. Malmberg, L. Cai. 2009. RNATOPS-W: A Web Server for RNA Structure Searches of Genomes. Bioinformatics, In press. doi:10.1093/bioinformatics/btp095
Momany, M., Pan, F. and R. Malmberg. 2008. Evolution and conserved domains of the septins. In The Septins (eds. P. Hall, H. Russell and J. Pringle), John Wiley and Sons Ltd., pages 35-45.
Huang, Z., Y. Wu, J. Robertson, L. Feng, R.L. Malmberg, L. Cai. 2008. Searching for non-coding RNA pseudoknot structures in genomes via graph tree decomposition. Bioinformatics, 24: 2281-2287
Zhao, J., R.L. Malmberg, L. Cai. 2008. Rapid ab initio RNA pseudoknot prediction via graph tree decomposition. Journal of Mathematical Biology, 56: 145-159
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.
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.
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.
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.
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.
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
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. 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. 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, 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.
Liu, C. M., Y. L. Song, R. L. Malmberg, and L. M. Cai. 2005. Profiling and searching for RNA pseudoknot structures in genomes. Proceedings of International Workshop in Bioinformatics Research and Applications (IWBRA 2005). Lecture Notes in Computer Science 3515: 968-975.
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.
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.
Malmberg, R. L., and R. Mauricio. 2005. QTL-based evidence for the role of epistasis in evolution. Genetical Research 86:89-95.
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.
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.
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.
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.
Malmberg, R. L. 2003. Plant mutagenesis and mutant screening Nature Encyclopedia of Life Sciences. London: Nature Publishing Group.
Cai, L., R. L. Malmberg, and Y. Wu. 2003. Stochastic modeling of RNA pseudoknotted structures: a grammatical approach. Bioinformatics 19:i66-i73.
Lawrence, C. J., R. L. Malmberg, M. G. Muszynski, and R. K. Dawe. 2002. Maximum likelihood methods reveal conservation of function among closely related kinesin families. Journal Of Molecular Evolution 54:42-53.
Malmberg, R. L., and J. Godwin. 2001. Replacement of an old HPLC integrator with an inexpensive computer and custom software. Biotechniques 30:1306-1308.

Welcome to the Malmberg Lab Web Site!

Ecological / Evolutionary Genetics with Sarracenia & NonCoding RNA Bioinformatics