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:
  • Stephens, J.D., Rogers, W.L., Heyduk, K., Cruse-Sanders, J.M., Determann, R.O., Glenn, T.C., and Malmberg, R.L. (2015). Resolving phylogenetic relationships of the recently radiated carnivorous plant genus Sarracenia using target enrichment. Molecular Phylogenetics and Evolution 85, 76-87.
  • Stephens, J.D., Rogers, W.L., Mason, C.M., Donovan, L.A., and Malmberg, R.L. (2015). Species Tree Estimation Of Diploid Helianthus (Asteraceae) Using Target Enrichment. American Journal of Botany 102, 910-920.
  • Wang, Y.F., Malmberg, R.L., and Cai, L. (2015). A Novel Structural Measure Separating Non-Coding RNAs from Genomic Backgrounds. Tsinghua University Science and Technology 20, 474-483.
  • Ding, L., Xue, X., LaMarca, S., Mohebbi, M., Samad, A., Malmberg, R.L., and Cai, L. (2015). Accurate prediction of RNA nucleotide interactions with backbone k-tree model. Bioinformatics 31, 2660-2667.
  • Alabady, M.S., Rogers, W.L., and Malmberg, R.L. (2015). Development of Transcriptomic Markers for Population Analysis using Restriction Site Associated RNA Sequencing (RARseq). Plos One.
  • Ding, L., Samad, A., Xue, X., Huang, X., Malmberg, R.L., and Cai, L. (2014). Stochastic k-Tree Grammar and Its Application in Biomolecular Structure Modeling 8th International Conference on Language and Automata Theory and Applications Lecture Notes in Computer Science 8370, 308-322.
  • Ding, L., Samad, A., Xue, X.R., Huang, X.Z., Malmberg, R.L., and Cai, L.M. (2014). Stochastic k-Tree Grammar and Its Application in Biomolecular Structure Modeling. In Language and Automata Theory and Applications, A.H. Dediu, C. MartinVide, J.L. SierraRodriguez, and B. Truthe, eds., pp. 308-322.
  • 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.
  • Ding, L., Robertson, J., Malmberg, R.L., and Cai, L. (2013). Protein Closed Loop Prediction from Contact Probabilities. In Bioinformatics Research and Applications, Z. Cai, O. Eulenstein, D. Janies, and D. Schwartz, eds. (Springer), pp. 199-210.
  • Manzourolajdad, 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.
  • 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.
  • 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.
  • Zhang, D., Xue, X.R., Malmberg, R.L., and Cai, L.M. (2012). TRFolder-W: a web server for telomerase RNA structure prediction in yeast genomes. Bioinformatics 28, 2696-2697.
  • 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.
  • 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.F., Malmberg, R.L., and Cai, L.M. (2011). Analyzing Modular RNA Structure Reveals Low Global Structural Entropy in MicroRNA Sequence. Journal of Bioinformatics and Computational Biology 9, 283-298.
  • Srivastava, A., Cai, L.M., Mrazek, J., and Malmberg, R.L. (2011). Mutational Patterns in RNA Secondary Structure Evolution Examined in Three RNA Families. Plos One 6.
  • Srivastava, A., Rogers, W.L., Breton, C.M., Cai, L.M., and Malmberg, R.L. (2011). Transcriptome Analysis of Sarracenia, an Insectivorous Plant. DNA Research 18, 253-261.
  • 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.
  • 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.
  • 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.
  • 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 2, 75-79.
  • 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, 145-155.
  • 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, 1080-1081.
  • 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, 2281-2287.
  • Momany, M., Pan, F., and Malmberg, R.L. (2008). Evolution and conserved domains of the septins. In The Septins, P. P. Hall, H. Russell, and J. Pringle, eds. (John Wiley and Sons), pp. 35-45.
  • Zhao, J.Z., Malmberg, R.L., and Cai, L.M. (2008). Rapid ab initio prediction of RNA pseudoknots via graph tree decomposition. Journal of Mathematical Biology 56, 145-159.
  • Brouillette, L.C., Rosenthal, D.M., Rieseberg, L.H., Lexer, C., Malmberg, R.L., and Donovan, L.A. (2007). Genetic architecture of leaf ecophysiological traits in Helianthus. Journal of Heredity 98, 142-146.
  • Pan, F.F., Malmberg, R.L., and Momany, M. (2007). Analysis of septins across kingdoms reveals orthology and new motifs. BMC Evolutionary Biology 7, 103.
  • Liu, 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., Liu, C.M., Malmberg, R.L., and Cai, L.M. (2006). Phylogenetic network inferences through efficient haplotyping. In Algorithms in Bioinformatics, Proceedings, pp. 68-79.
  • Song, Y., Liu, C., Malmberg, R.L., He, C., and Cai, L. (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.L., Liu, C.M., Huang, X.Z., Malmberg, R.L., Xu, Y., and Cai, L.M. (2006). Efficient parameterized algorithms for biopolymer structure-sequence alignment. IEEE-ACM Transactions on Computational Biology and Bioinformatics 3, 423-432.
  • Song, Y., Liu, C., Huang, X., Malmberg, R.L., Xu, Y., and Cai, L. (2006). Efficient parameterized algorithms for biopolymer structure-sequence alignment. Ieee-Acm Transactions on Computational Biology and Bioinformatics 3, 423-432.
  • 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.
  • 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, pp. 262-273.