, Bioinformation Engineering Laboratory, Department of Biotechnology, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Japan

• Journal of Nucleic Acids Investigation Vol. 4 No. 1 (2013) - Articles
  A new entropy model for RNA: part II. Persistence-related entropic contributions to RNA secondary structure free energy calculations
  Abstract  PDF  APPENDIX
• Journal of Nucleic Acids Investigation Vol. 5 No. 1 (2014) - Early Release
  A new entropy model for RNA: part IV, The Minimum Free Energy (mFE) and the thermodynamically most-probable folding pathway (TMPFP)
  Abstract  PDF  Supplement S2: Methods: the vsfold5 algorithm  Prediction of RNA Pseudoknots Using Heuristic Modeling with Mapping and Sequential Folding
• Journal of Nucleic Acids Investigation Vol. 5 No. 1 (2014) - Early Release
  A new entropy model for RNA: part V, Incorporating the Flory-Huggins model in structure prediction and folding
  Abstract  PDF