Research

This laboratory studies the following topics on a PC cluster in the lab with the infinite spirit and imagination of the students. The topics are grouped into two axes. The first axis has its base on the biological questions, and it aims to solve the biological phenomena by applying the existing computational methods. In case that the existing methods do not fit, we might develop new methods by ourselves. Another axis has its base on the technical questions and aims improvement of the existing computational biology’s methods as well as development of new methods. In fact, single topic has both aspects, but the student tends to have a main axis out of the two. The preference of each student determines the axis in focus. The lab as a whole  has its base on the biological questions and often develops new technologies out of necessity.

The 1st Axis: The Molecular Biology Questions

  • RNA modification process in eukaryotic cells
    • Splicing
      • Mechanism of splicing on spliceosome
      • Origin of intron
        • Correlation between protein 3D structures and genome structures
      • Alternative splicing
        • 3D structure of isoforms
        • Exon selection mechanisms
    • RNA editing
      • Effect of editing on protein 3D structure
      • Selection mechanisms of editing site
  • Radiation resistant mechanisms of Deinococcus radiodurans
  • Heat resistant mechanisms of Thermus thermophilus
 

The 2nd Axis: The Technological Development in Computational Biology

  • Accurate comparative modeling method
  • Predict docked structures of biomolecules
    • Protein-RNA
    • Protein-DNA
    • Protein-Protein
    • Protein-ligand
  • Predict RNA 3D structure
  • Database building for DNA repair-related proteins
  • Predict protein function from amino acid sequence and protein 3D structure

Not all the topics are developed at the same pace, and there are some topics that are dormant for a while.

Because most of the topics are studied in collaboration with external researchers, one should not be taciturn and should be communicative. Especially for the research consultation with specialists in different fields, it is essential to have the ability to understand what they say, to communicate what you do not understand, and to tell your research contents in an understandable manner to them. In short, one should understand that the perspective to the world of each researcher is completely different, once the scientific background is different.