Will Rogers 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. Liming Cai

Recent Publications:
  • Srivastava, A., Zhang, X., LaMarca, S., Cai, L., and Malmberg, R.L. (2013). Patterns of chromatin-modifications discriminate different genomic features in Arabidopsis. Tsinghua Science and Technology 18, 431-440
  • 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 http://dx.doi.org/10.1016/j.jtbi.2012.10.023,.
  • Ding, L., Robertson, J., Malmberg, R.L., and Cai, L. (2013). Protein closed loop prediction from contact probabilities. In Bioinformatics research and applications, Cai, Z., Eulenstein, O., Janies, D., and Schwartz, D., eds. (Springer), pp. 199-210.
  • 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, 2696-2697 doi: 10.1093/bioinformatics/bts506.
  • 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 10.1186/1471-2105-13-s5-s1.
  • 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, 1162–1180 DOI: 10.1002/ece3.262.
  • Shareghi, P., Wang, Y., Malmberg, R.L., and Cai, L. (2012). Simultaneous prediction of RNA secondary structure and helix coaxial stacking. BMC Genomics 13, S7 doi: 10.1186/1471-2164-13-S3-S7.
  • 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, 184-189 10.1109/ICCABS.2011.5729876.
  • Srivastava, A., Rogers, W.L., Breton, C.M., Cai, L., and Malmberg, R.L. (2011). Transcriptome analysis of Sarracenia, an insectivorous plant. DNA Research, 1-9 10.1093/dnares/dsr014.
  • Srivastava, A., Cai, L., Mrázek, J., and Malmberg, R.L. (2011). Mutational patterns in RNA secondary structure evolution examined in three RNA families. PLOS One 6, e20484 10.1371/journal.pone.0020484.
  • 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 sequence. Journal of Bioinformatics and Computational Biology 9, 283-298 10.1142/S0219720011005495.
  • 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.
  • 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, 571-583.
  • Shaw, T.I., Manzour, A., Wang, Y., Malmberg, R.L., and Cai, L. (2010). Analyzing modular RNA structure through shannon entropy reveals low global structural entropy in mirnas. CSB Conference Proceedings 9, 146-155.
  • 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.
  • Rogers, W.L., Cruse-Sanders, J.M., Determann, R., and Malmberg, R.L. (2010). Development and characterization of microsatellite markers in Sarracenia L. (pitcher plant) species. Conservation Genetics Resources, DOI: 10.1007/s12686-009-9165-x .
  • 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.