2016 Advanced Bioinformatics

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Academic unit or major
Fukui Toshiaki  Oota Motonori  Ohta Hiroyuki  Sakurai Minoru  Yamada Takuji  Konagaya Akihiko 
Course component(s)
Day/Period(Room No.)
Intensive ()  
Course number
Academic year
Offered quarter
Syllabus updated
Lecture notes updated
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Course description and aims

Through recent improvements in DNA sequencing technology, DNA base sequences and amino-acid sequences of proteins are increasing explosively, and bioinformatics, which handles this biological information has become an important field. In this course we will cover the basics and applications of bioinformatics from a life science and computational science viewpoint. The instructor will start by teaching the basics of molecular biology for students not in the biology field. The instructor will then go over microbial genome analysis, analysis of amino-acid sequences of proteins, proteinomics that uses computational science, plant science that uses bioinformatics, metagenome analysis, and DNA computers.

Student learning outcomes

By the end of this course, students will be able to:
1. Understand the fundamentals of molecular biology
2. Explain the outline of bioinformatics
3. Acquire advanced knowledge of research fields using bioinformatics


Bioinformatics, Molecular biology, Genome analysis, , Homology search, Stereostructure prediction, Molecular orbital calculation, Molecular mechanics calculation, Molecular dynamics simulation, Transcriptome, Coexpression analysis, Plant hormone, Metagenome, Synthetic biology, Constructive approach

Competencies that will be developed

Specialist skills Intercultural skills Communication skills Critical thinking skills Practical and/or problem-solving skills

Class flow

Each of 6 instructors provide one class, and elaborate on the selected topic using PowerPoint slides.

Course schedule/Required learning

  Course schedule Required learning
Class 1 Fundamentals of molecular biology, and genome analysis of microbes (Fukui) Understand fundamentals of molecular biology, and explain the notion and methodologies of genome analysis of microbes.
Class 2 Homology search and structure prediction for proteins (M. Ohta) Understand the homology search method for proteins and apply it to the structure prediction.
Class 3 Application of computational chemistry to protein science (Sakurai) Understand the current status of the application of molecular orbital calculation and molecular dynamics simulation to protein science.
Class 4 Application of bioinformatic approach for research in plant science Understand how bioinformatic approach is applied for research in plant science.
Class 5 Fundamentals and applications of metagenomics (Kurokawa) Understand fundamentals of metagenomics.
Class 6 Creation of DNA computer and “life” (Kiga) Understand notion of synthetic biology, and explain examples of artificial systems consisting of biomacromolecules.



Reference books, course materials, etc.

Materials are distributed as needed at the beginning of lecture. PowerPoint slides used in lecture are uploaded to OCWi in advance when possible.

Assessment criteria and methods

Students are evaluated on the total from quizzes in each lecture.

Related courses

  • None

Prerequisites (i.e., required knowledge, skills, courses, etc.)



This course is provided as a course in "Medical and Dental Engineering Special Course" held by Joint Program between Tokyo Institute of Technology - Tokyo Medical and Dental University. This course will be opened at Campus Innovation Center (Tamachi Campus) in specific week(s) in August-October. One class is 135 min. The detailed schedule will be available in HP of this special course.

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