Computational Biology Research Center[CBRC]

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

website

Key Words

Machine learning, Kernel methods, Protein networks, Structured data

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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).