Non-coding RNAs

Non-coding RNAs (ncRNAs) play critical roles in biology. We study ncRNA structure predictions and ncRNA gene search.

Citation

  • Yingfeng Wang, Russell L. Malmberg, and Liming Cai, “A Novel Structural Measure Separating Non-Coding RNAs from Genomic Backgrounds,” Tsinghua Science and Technology, vol. 20, no. 5. pp. 474-483, 2015.
  • Amirhossein Manzourolajdad, Yingfeng Wang, Timothy I. Shaw, and Russell L. Malmberg, “Information-theoretic Uncertainty of SCFG-modeled Folding Space of the Non-coding RNA,” Journal of Theoretical Biology, vol 318, pp 140-163, 2013.
  • Pooya Shareghi, YingfengWang, Russell L. Malmberg, and Liming Cai, “Simultaneous Prediction of RNA Secondary Structure and Helix Coaxial Stacking,” BMC Genomics, vol 13, Suppl 3 S7, 2012.
  • Yingfeng Wang, Amir Manzour, Pooya Shareghi, Timothy I. Shaw, Ying-Wai Li, Russell L. Malmberg, and Liming Cai, “Stable Stem Enabled Shannon Entropies Distinguish Noncoding RNAs from Random Backgrounds,” BMC Bioinformatics, vol 13, Suppl 5 S1, 2012.
  • Timothy I. Shaw, Amir Manzour, Yingfeng Wang, Russell L. Malmberg, and Liming Cai, “Analyzing Modular RNA Structure Reveals Low Global Structural Entropy in MicroRNA Sequence,” Journal of Bioinformatics and Computational Biology, vol.9, no.2, pp.283-298, 2011.
  • Leilei Guo, Dong Zhang, Yingfeng Wang, Russell L. Malmberg, Michael J. McEachern, and Liming Cai, “TRFolder: Computational Prediction of Novel Telomerase RNA Structures in Yeast Genomes,” International Journal of Bioinformatics Research and Applications, vol.7, no.1, pp.63-81, 2011.
  • Pooya Shareghi, Yingfeng Wang, Russell L. Malmberg, and Liming Cai, “Simultaneous Prediction of RNA Secondary Structure and Helix Coaxial Stacking,” Proceedings of 2011 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp.89-95, Nov. 2011.
  • Yingfeng Wang, Amir Manzour, Pooya Shareghi, Timothy I. Shaw, Ying-Wai Li, Russell L.Malmberg, and Liming Cai, “Stable Stem Enabled Shannon Entropies Distinguish Noncoding RNAs from Random Backgrounds,” Proceedings of 1st IEEE International Conference on Computational Advances in Bio and medical Sciences (ICCABS), pp.184-189, Feb. 2011.
  • Timothy I. Shaw, Amir Manzour, Russell L. Malmberg, Yingfeng Wang, and Liming Cai, “Analyzing Modular RNA Structure Reveals Low Global Structural Entropy in MicroRNA Sequence,” Proceedings of 9th Annual International Conference on Computational Systems Bioinformatics (CSB), pp. 146-155, Aug. 2010.
  • Yingfeng Wang, Zhibin Huang, Yong Wu, Russell L. Malmberg, and Liming Cai, “RNATOPS-W: A Web Server for RNA Structure Searches of Genomes,” Bioinformatics, vol. 25, no. 8, pp. 1080-1081, 2009.