Computational Biology Research Center[CBRC]

Advanced Industrial Science and Technology[AIST]
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Machine Learning Research Group

We are working to develop novel algorithms for use in molecular biology and drug discovery. Our main areas of interest include:


Research Topics

Privacy-preserving search in chemical compound databases
Comprehensive analysis of millions of ligand-binding pockets based on efficient all pairs similarity search
Fast clustering of massive short reads by multiple sorting
Machine learning methods for activity recognition from biomedical sensor data



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Team Member

Koji Tsuda
Senior Research Scientist E-mail
Koji Tsuda
Key Words

Machine learning, Kernel methods, Protein networks, Structured data


David Du Verle
JSPS
Fellow
E-mail
Key Words

machine learning, gene expression analysis, time series analysis, gene regulatory network inference


Papers List

  • J. Ito, Y. Tabei, K. Shimizu, K. Tomii and K. Tsuda: "PDB-scale Analysis of Known and Putative Ligand-binding Sites with Structural Sketches", Proteins, 80:747-763, (2012).
  • Y. Tabei and K. Tsuda. SketchSort: "Fast All Pairs Similarity Search for Large Databases of Molecular Fingerprints.", Molecular Informatics, 30(9):801-807, 2011.
  • K. Shimizu and K. Tsuda. SlideSort: "All Pairs Similarity Search for Short Reads.", Bioinformatics, 27(4):464-470, (2011).
  • E. Georgii, K. Tsuda and B. Schoelkopf: "Multi-way Set Enumeration in Weight Tensors", Machine Learning, 82(2):123-155, (2011).
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