Publications

Publications listed here have been co-authored by the RNA-Informatics Group members, covering a wide range of research topics in RNA informatics and other projects in bioinformatics, algorithms and theory of computing. They are listed in the reversed chronicle order.

2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005


2012

  • [Shareghi et al, 2012] Shareghi, P., Wang, Y., Malmberg, R., and Cai, L. (2012) Simultaneous prediction of RNA secondary structure and helix coaxial stacking, BMC Genomics, 13(Suppl 3): S7, doi: 10.1186/1471-2164-13-S3-S7.
  • [Wang et al, 2012] Wang, Y., Manzour, A., Shareghi, P., Shaw, T., Li., Y., Malmberg, R., and Cai, L. (2012) Stable stem enabled Shannon entropies distinguish non-coding RNAs from random backgrounds, BMC Bioinformatics, 13(Suppl 5): S1, doi: 10.1186/1471-2105-13-S5-S1.
  • [Zhang et al, 2012] Zhang, D., Xue, X., Y., Malmberg, R., and Cai, L. (2012) TRFolder-W: A Web Server for Telomerase RNA Structure Prediction, Bioinformatics, accepted.
  • [Wang et al, 2012a] Wang, Y., Malmberg R., and Cai, L. (2012) A novel structural measure separating non-coding RNAs from genomic backgrounds. submitted

2011

  • [Shareghi et al, 2011] Shareghi, P., Wang, Y., Malmberg, R., and Cai, L. (2011) Simultaneous prediction of RNA secondary structure and helix coaxial stacking, Proceedings of 2011 IEEE International Conferences on Bioinformatics & Biomedicine, pp. 89-95.
  • [Guo et al, 2011] Guo, L., Zhang, D., Wang, Y., Malmberg, R.L., McEarchen, M., and Cai, L. (2011) TRFolder: Computational Prediction of Novel Telomerase RNA Structures in Yeast Genomes, International Journal of Bioinformatics Research and Applications, Vol. 7, No. 1, 63-81.
  • [Wang et al, 2011] Wang, Y., Manzour, A., Shareghi, P., Shaw, T., Li., Y., Malmberg, R., and Cai, L. (2011) Stable stem enabled Shannon entropies distinguish non-coding RNAs from random backgrounds, in The Proceedings of 1st IEEE International Conference on Computational Advances in Bio and medical Sciences (ICCABS), 184-189.
  • [Shaw et al, 2011] Shaw, T., Manzour, A., Wang, Y., Malmberg, R., and Cai, L. (2011) Analyzing modular RNA structure reveals low global structural entropy in microRNA sequences, Journal of Bioinformatics and Computational Biology, 9(2):283-98.
  • [Srivastava et al, 2011a] Srivastava, A., Cai, L., Mrazek, J., and Malmberg R.L., (2011) Mutational Patterns in RNA Secondary Structure Evolution Examined in Three RNA Families. PLoS ONE 6(6): e20484. doi:10.1371/journal.pone.0020484
  • [Srivastava et al, 2011b] Srivastava, A., Rogers, W.L., Breton, C.M., Cai, L. and Malmberg, R.L. (2011) Transcriptome Analysis of Sarracenia, an Insectivorous Plant. DNA Research; doi: 10.1093/dnares/dsr014
  • [Srivastava et al, 2011c]Srivastava, A. Zhang, X., LaMarca, S., Cai, L., and Malmberg, LR. (2011) Patterns of Chromatin-Modifications Discriminate Different Genomic Features in Arabidopsis, submitted.

2010

  • [Huang et al, 2010] Huang, Z., Mohebbi M., Malmberg, R., and Cai, L. (2010) RNAv: Non-coding RNA Secondary Structure Variation Search via Graph Homomorphism, Proceedings of Computational Systems Bioinformatics Conference (CSB2010), Vol. 9, p. 56-69.
  • [Malmberg, et al, 2010] Malmberg, R., Shaw, T., and Cai, L. (2010) RNApasta: a tool for analysis of RNA structural alignments, Journal of Bioinforamtics Research and Applications, Vol 6 No 6, 571-583.
  • [Huang and Cai, 2010] Huang, X. and Cai, L. (2010) Fixed-parameter approximation: conceptual framework and approximability results, Algorithmica, 57(2), 398-407.
  • [Shaw et al, 2010] Shaw, T., Manzour, A., Wang, Y., Malmberg, R., and Cai, L. (2010) Analyzing modular RNA structure reveals low global structural entropy in microRNA sequences, Proceedings of Computational Systems Bioinformatics Conference (CSB2010), Vol. 9, p. 146-155.

2009

  • [Wang et al., 2009] Wang, Y., Huang, Z., Wu, Y., Malmberg, R., and Cai, L. (2009) RNATOPS-W: a web server for RNA pseudoknot search, Bioinformatics, accepted.
  • [Malmberg, et al., 2009] Malmberg, R., Shaw, T., and Cai, L. (2009) RNApasta: a computational tool for analysis of RNA alignments, used to resolve phylogenetic variation in mir-31 RNAs, submitted.

2008

  • [Huang et al., 2008] Huang, Z., Wu, Y., Robertson, J., Feng, L., Malmberg, R., and Cai, L. (2008) Fast and accurate search for non-coding RNA pseudoknot structures in genomes, Bioinforamtics, 24(20):2281-2287.
  • [Huang, et al., 2008a] Cai, L., Huang, X., Liu, C., Rosamond, F., and Song, Y. (2008) Parameterized complexity and biopolymer sequence comparison, The Computer Journal, Special Issue in Parameterized Complexity, 51(3): 270-291.
  • [Liu et al., 2008] Liu, C., Song, Y., Yan, B., Xu, Y., and Cai, L. (2008) Fast de novo peptide sequencing and spectral alignment via tree decomposition, International Journal of Computational Science, Special Issue on Bioinformatics and Computational Biology, in press.
  • [Zhao et al., , 2008] Zhao, Z., Malmberg, R., and Cai, L. (2008) Rapid ab initio prediction of RNA pseudoknots via graph tree decomposition, Journal of Mathematical Biology, Special Issue in RNA, Vol 56, No: 1-2, 145-159
  • [Momany et al., 2008] 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., in press.

2007

  • [Zhao et al., 2007a] Zhao, J., Che, D., and Cai, L. (2007) Comparative pathway annotation with protein-DNA interaction and operon information via graph tree decomposition, Proceedings of Pacific Symposium on Biocomputing (PSB 2007), 12:496-507,
  • [Che et al., 2007] Che, D., Zha, J., Xu, Y., and Cai, L. (2007) Operon prediction in microbial genomes using decision tree approach, Proceedings of IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB 2007), 135-142, also to appear in International Journal of Information Technology and Intelligent Computing.
  • [Zhao et al,. 2007b] Zhao, J., Che, D., and Cai, L. (2007) Comparative pathway prediction with structural genomic information via a unified graph Model, Proceedings of 2007 International Symposium on Bioinformatics Research and Applications (ISBRA 2007), 627-637.
  • [Huang et al,. 2007] Huang, X., Hood, E., and Cai, L. (2007) Protein tertiary structure prediction by protein threading: a survey, Plant Biotechnology Journal, to appear.
  • [Cai et al., 2007] Cai, L., Fellows, M., Juedes, and D., Rosamond, F. (2007) The complexity of polynomial-time approximation, Theory of Computing Systems (formerly Mathematical Systems Theory), Vol 41, No 3, pp. 459-477.
  • [Pan et al., 2007] Pan, F., Malmberg, R., Momany, M. (2007). Evolution of the septins: orthology across kingdoms and identification of new motifs. BMC Evolutionary Biology 7:103.
  • [Pan et al., 2007a] Pan F., Che D., Momany M., Cai L. and Malmberg R.L. (2007) Protein co-evolution and its applications in residue contact prediction, manuscript.

2006

  • [Liu et al., 2006a] Liu, C., Yan, B., Song, Y., Xu, Y., and Cai, L. (2006) Tag-based blind PTM identification with point process model, Proceedings of International Symposium on Intelligent Systems for Molecular Biology (ISMB 2006), Fortaleza, Brazil, also in Bioinformatics, Vol 22, No 14, (with), 307-313, 2006.
  • [Song et al., 2006a] Song, Y., Liu, C., Huang, X., Malmberg, R., Xu, Y., and Cai, L. (2006) Efficient parameterized algorithms for biopolymer structure-sequence alignment", IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol 3, No. 4, 423-431.
  • [Liu et al., 2006b] Liu, C., Song, Y., Hu, P., Malmberg, R., and Cai, L. (2006) Efficient annotation of non-coding RNA structures including pseudoknots via automated filters, Proceedings of Life Science Society Computational Systems Biology Conference (CSB 2006), Palo Alto, California, 99-110.
  • [Xu et al., 2006] Xu, Y., Liu, Z., Cai, L., and Xu, D. (2006) Protein structure prediction by protein threading, in Computational Methods for Protein Structure Prediction and Modeling, Vols I&II, (eds. Xu, Y., Xu, D., and Liang, J.), 389-430, Springer.
  • [Zhao et al., 2006a] Zhao, J., Malmberg, R., and Cai, L. (2006) Rapid ab initio RNA folding including pseudoknots via graph tree decomposition, Proceedings of the 6th Workshop on Algorithms in Bioinformatics (WABI 2006), Lecture Notes in Bioinformatics 4175, Zurich, Switzerland, 262-273.
  • [Song et al., 2006b] Song, Y., Liu, C., Malmberg, R., and Cai, L. (2006) Phylogenetic network inferences through efficient haplotyping, Proceedings of Workshop on Algorithms in Bioinformatics (WABI 2006), Lecture Notes in Bioinformatics 4175, Zurich, Switzerland, 68-79.
  • [Huang and Cai, 2006] Huang, X. and Cai, L. (2006) Fixed-parameter approximation: conceptual framework and approximability results, Proceedings of the 2nd International Workshop on Parameterized and Exact Computation, Zurich, Switzerland, Lecture Notes in Computer Science 4169, 96-108.
  • [Song et al., 2006c] Song, Y., Liu, C., Malmberg, R., 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, Vol. 2, No. 3, 289-304.
  • [Zhao et al., 2006b] Zhao, J., Malmberg, R., and Cai, L. (2006) Learning the parameters of stochastic grammar models for RNA structures with pseudoknots, Proceeding of IEEE International Conference on Granular Computing (IEEE GrC 2006), Atlanta, 170-175.
  • [Liu et al., 2006] Liu, C., Song, Y., Yan, B., Xu, Y., and Cai, L. (2006) Fast de novo peptide sequencing and spectral alignment via tree decomposition, Proceedings of Pacific Symposium on Biocomputing (PSB 2006), 255-266, Hawaii.

2005

  • [Song et al., 2005a] Song, Y., Liu, C.,, Malmberg, R., Pan, F., and Cai, L., (2005) Tree decomposition-based fast RNA pseudoknot search in genomes, Proceedings of IEEE Computer Society Computational Systems Bioinformatics Conference, (CSB 2005), 223-234, Palo Alto.
  • [Liu et al., 2005a] Liu, C., Song, Y., Malmberg, R., and Cai, L. (2005) Profiling and searching for RNA pseudoknot structure in genomes, Transactions on Computational Systems Biology 2: 37-47.
  • [Che et al., 2005] Che, D., Jensen, S., Cai, L., Liu, J.S. (2005) BEST: Binding-site estimation suite of tools, Bioinformatics 21(12): 2909-2911.
  • [Song et al., 2005b] Song, Y., Liu, C., Huang, X., Malmberg, R., Xu, Y., and Cai, L. (2005) Efficient parameterized algorithms for biopolymer structure-sequence alignment, Proceedings of Workshop on Algorithms in Bioinformatics (WABI 2005), Mallorca, Spain, Lecture Notes in Bioinformatics 3692: 376-388.
  • [Song et al., 2005c] Song, Y., Zhao, J., Liu, C., Liu, K., Malmberg, R., and Cai, L. (2005) RNA structural homology search with a succinct stochastic grammar model, Journal of Computer Science and Technology Vol.20, No.4, Special Issue in Bioinformatics, 454-464.
  • [Liu et al., 2005b] Liu, C., Song, Y., Malmberg, R., and Cai, L. (2005) Profiling and searching for RNA pseudoknot structure in genomes, Proceedings of International Workshop in Bioinformatics Research and Applications (IWBRA 2005), Lecture Notes in Computer Science 3515: 968-975.