2024 Faculty Courses School of Life Science and Technology Undergraduate major in Life Science and Technology
Bioinformatics(LST)
- Academic unit or major
- Undergraduate major in Life Science and Technology
- Instructor(s)
- Akio Kitao / Takuji Yamada
- Class Format
- Lecture (Face-to-face)
- Media-enhanced courses
- -
- Day of week/Period
(Classrooms) - 3-4 Tue / 3-4 Fri
- Class
- -
- Course Code
- LST.A246
- Number of credits
- 200
- Course offered
- 2024
- Offered quarter
- 4Q
- Syllabus updated
- Mar 17, 2025
- Language
- Japanese
Syllabus
Course overview and goals
This course focuses on the basics of bioinformatics, which is an integrated field of life science, information science, and statistical mechanics.
Yamada: Understanding basics of bioinformatics for genome and metagenome analyses (6 lectures)
Kitao: Learning statistical mechanics to connect biological microscopic states and macroscopic states (8 lectures)
Course description and aims
Yamada: Understanding basics of bioinformatics
Kitao: Understanding the relation between statistical mechanics and biological phenomena
Keywords
Bioinformatics, database, sequence analysis, phylogenetic analysis
Physical Chemitry, thermodynancs, statistical mechanics, biophysics
Competencies
- Specialist skills
- Intercultural skills
- Communication skills
- Critical thinking skills
- Practical and/or problem-solving skills
Class flow
Lecture is given for each topic, followed by some practices when necessary.
Course schedule/Objectives
| Course schedule | Objectives | |
|---|---|---|
| Class 1 | Introduction to bioinformatics (Yamada 1) | Tools, databases and their significance |
| Class 2 | Genome and gene (Yamada 2) | Concept of gene, gene structure annotation, gene function annotation |
| Class 3 | Large-scale experiments for bioinformatics (Yamada 3) | DNA sequencer and its principle |
| Class 4 | Metagenome analysis: shotgun and 16S (Yamada 4) | Concept of metagenome, understanding of phylogenetics and its assignement, gene function annotation |
| Class 5 | Statistical analysis in genome/metagenome analysis (Yamada 5) | Statistics, concept of statistical test, comparison between groups |
| Class 6 | Machine learning in bioinformatics (Yamada 6) | Applications of machine learning in life science |
| Class 7 | Microscopic states and probability (Kitao 1) | Understand probability and macroscopic and microscopic states in biological systems |
| Class 8 | Microscopic states and probability (Kitao 2) | Understand the relation between probability and microscopic states |
| Class 9 | Introduction to statistical ensembles 1 (Kitao 3) | Understanding microcanonical ensemble |
| Class 10 | Introduction to statistical ensembles 2 (Kitao 4) | Understanding canonical ensemble |
| Class 11 | Introduction to statistical ensembles 3 (Kitao 5) | Understanding other ensembles |
| Class 12 | Applications of statistical ensembles 1 (Kitao 6) | Understanding of some applications of statistical ensembles including two-state model |
| Class 13 | Applications of statistical ensembles ２ (Kitao 7) | Understanding of some applications of statistical ensembles including two-state chain molecular model |
| Class 14 | Applications of statistical ensembles ３ (Kitao 8) | Understanding of some applications of statistical ensembles including harmonic oscillator |
Study advice (preparation and review)
To enhance effective learning, students are encouraged to spend approximately 100 minutes preparing for class and another 100 minutes reviewing class content afterwards (including assignments) for each class.
They should do so by referring to textbooks and other course material.
Textbook(s)
None.
Reference books, course materials, etc.
Japanese Society of Bioinformatics. Bioinformatics Nyumon (Japanese), ISBN-13: 978-4766422511
David Mount. Bioinformatics: Sequence and Genome Analysis 2nd Edition, ISBN-13: 978-0879697129
Donald A. McQuarrie, Statistical Mechanics ISBN-13: 978-8130918938
Evaluation methods and criteria
Evaluation of assignments imposed during the lecture and those submitted after the lecture.
Related courses
- LST.A241 ： Biostatistics
- LST.A351 ： Genome Informatics
- LST.A201 ： Physical Chemistry I
- LST.A206 ： Physical Chemistry II
- LST.A211 ： Physical Chemistry III
- LST.A341 ： Biophysical Chemistry
Prerequisites
None.