Division of Bioengineering and Bioinformatics Graduate School of Information Science and Technology, Hokkaido University | Bioengineering and Bioinformatics Course Department of Electronics and Information Engineering School of Engineering, Hokkaido University

Laboratories

Information Biology

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Laboratory outline

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Prediction of ligands for orphan olfactory receptors based on classification by self-organizing map

The genomes of humans and various other organisms have been sequenced. However, genomic information, or the life-codes, has yet to be deciphered. In our laboratory, we focus on revealing the structure, function and evolution of genes and proteins. For this purpose, we explore the universe of a human body and other living organisms to develop various applications in medicine, drug design, and agriculture.

Introduction of research content

All living organisms, known so far, carry genetic materials in the form of nucleic acids (DNA, RNA) as the blueprints of life. A virtually atomic element is called a gene, and a set of genes used to constitute a living organism is called a genome. The human genome sequencing is almost completed to describe merely three billion base pairs, but its real meaning has yet to be determined. This is analogical to predict the functional behavior of aircraft and its parts based on the design drawings of component only.

Biology has gotten into the era of information analysis. This is because we do not yet know how the microscopic parts constitute the functional networks to lead the macroscopic behaviors of organism, even though the parts information and the living samples are easily accessible. This is the key for understanding the hardest core of life and overcoming diseases. Our laboratory conducts researches based on genetic information and its alternative form of proteins to clarify the constitutive principles of structure, function, and behavior in networks, biodiversity, molecular phylogeny of biomolecules to understand the total design of life. Students are expected to choose any topics for their research concerning to the field. The examples include:

  • Research and application on molecular evolution, natural selection and evolutionary rates
  • Structural prediction and functional design of biomolecules
  • Researches on the evolution and biodiversity of the brain, central nervous system, sensors and their applications
  • Development of databases and algorithms that can deal with large-scale biological information
  • Development of algorithms for genetic diagnosis and drug efficacy prediction

Research methods

Analysis based on statistics and evolutionary process of genes and proteins

Though the genes have the same function, there are differences between genes in different organisms and individuals. These differences can lead to find the cause of diseases and their unique functions specific to the organisms or individuals, but we cannot examine them directly and visually. Therefore, we use computers to examine those features such as the parts of the gene evolved and the history of the genes and organisms.

Analysis, prediction and simulation of three dimensional protein structures

Since the protein is too small, the structure of proteins is actually invisible. However, we can virtually display those structures on the computer. It can be make us possible to find potential drug compounds and check their reaction by combining them with receptor proteins.

Integrating approach between information science and biology

We are surrounded by enormous amount of information, and it is not limited only to biological information. In the field of information science, algorithms to efficiently manage the information are widely studied. It is attracting to apply those technologies to various biological problems. This integration is an emerging approach to solve longstanding problems in the biology.

Examples of research equipment

PCs for individual use, Linux servers, GPGPU hardware, MATLAB bioinformatics tools, etc.

Knowledge and technologies that will be useful in the future

Basic skills related to computer operations

  • Basic skills in the Linux/unix environment such as server management
  • Programming skill
  • Basic skills related to database operations

Basic knowledge and skills related to statistics and data processing

  • Skills related to statistical analysis using statistics analysis software such as R and Matlab
  • Statistics and data processing skill using self-produced programs

Skills related to life information analysis

  • Skills to manage information on genes and proteins
  • Protein structure prediction, visualization and manipulation skills
  • Molecular evolutionary analysis, molecular phylogenetic analysis

People who are interested in these key words, please visit this laboratory.

Molecular evolution, conservation and differentiation of structures and functions, biodiversity, evolution and divergence of senses, algorithms, machine learning, brain/nervous system, diseases, drug discovery, biological information database

Members

  • Professor: Toshinori Endo
  • Associate Professor: Katsuhiko Mineta

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Contact

Address: Room 9-25 (Professor), Room 9-24 (Associate Professor), 9-07/08/09 (laboratories)
Graduate School of Information Science and Technology, Hokkaido University
Kita 14-jo, Nishi 9-chome, Kita-ku, Sapporo, 060-0814
Extension: 6547 (Prof. Endo); 7332 (Associate Prof. Mineta)

Tel.: 011-706-6547 (Prof. Endo); 011-706-7332 (Associate Prof. Mineta)

E-mail: endo@ibio.jp (Prof. Endo); mineta@ibio.jp (Associate Prof. Mineta)

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