Shibuya Laboratory

About This Laboratory

We are interested in developing efficient (and accurate) algorithms and software for computational problems in molecular biology. Many of these problems are very complicated and difficult problems. Moreover, the data in the field has been increasing exponentially, due to the recent development of technologies, such as DNA sequencing, SNP typing, and NMR. Thus, sophisticated algorithm design and development are almost mandatory in the field. Our recent work includes sequence alignment, sequence database searching, gene finding, analysis of SNPs, pathway analysis, 3-D protein structure database searching, 3-D protein function prediction, and so on. Many of these problems require wide knowledge of computer science, such as combinatorial pattern matching, learning, graph theory. We believe it would be great fun to do algorithmic research in the field especially for computer scientists.
Research topics in our lab:

Algorithms in Computational Biology / Bioinformatics
- Indexing algorithms for protein structure databases
- Structural analysis of proteins/RNAs
- Sequence alignment / indexing
- Sequence analysis (Analysis of next-generation sequencers, gene finding, RNAi prediction, etc)
- DNA assembly
- SNP analysis
- etc.
Algorithms and Theory
- Combinatorial pattern matching
- SMAD
- Database search
- Data compression
- Graph and network analysis
- Learning theory
- etc.

Members

Staffs
- Tetsuo Shibuya (Associate Professor)
- Hiroko Tanaka (Technical staff)
- Georg Chalkidis (Technical staff)
Students
- Sahli Mohammed (D2)
- Atsushi Hashimoto (D1)
- He Li (M2)
- Hideharu Hiratsuka (M2)
- Hiroyuki Ohga (M2)
- Taku Onodera (M2)
- Chen Jing (M2)
Alumni
- Ritsuko Onuki （2005-2011）
- Michael Wilson (2010-2011)
- Ben Hachimori (2007-2009)
- Koichi Suematsu （2005-2008）
- Chia-han Chu (2007)
- Hiroki Sakai (2004-2007)

Software tools developed in our lab

DNAScissor
- An easy-to-use tool for preprocessing sequence reads from sequencers with splendid GUI.
Arapan
- Sequence assembler

To be a Member of Our Laboratory

We welcome anyone who are willing to do research with us as a master course student or a ph.D. candidate. To enroll into the master/ph.D course, you need to take the entrance examination of the Department of Computer Science, Graduate School of Information Science and Technology, University of Tokyo. Please take a look at these links, as these web pages provide not only the administration info but also the problems in the past exams. Please feel free to contact/visit us before applying for the exam.

Admission Information
- Admission information by Graduate School of Information Science and Technology
- Admission information by Department of Computer Science　(This page includes past exams on computer science)
- Past exams on mathematics

Contact

Address
- Laboratory of Sequence Analysis, Human Genome Center, University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, JAPAN.
- Location (Our building is located at the 4th floor of the building No. 2 in the map. Call ext. 75791 at the entrance)
Phone: +81-3-5449-5791/+81-3-5449-5793 Fax: +81-3-5449-5790