IISTIIST (Institute of Integrated Science and Technology)

This introductory course is offered to students in general, with diverse background. No previous knowledge of molecular biology or chemistry,　although recommended, is not required, as most basic　topics will be presented in a concise manner at the beginning of the course. Processes covering from gathering scientific information, to sequencing of genomic material will be presented.

After the completion of this course, the student should be able:
(1) to understand the basic concepts and principles of bioinformatics, and how they are applied routinely;
(2) to acquire basic and relevant information in the literature
by cross-referencing;
(3) to retrieve and analyze genomic and protein sequences from
their respective databases; and
(4) to interpret the processed data;
(5) to understand the basic concepts of evolution, and the assessment of current times.

英語 / English

This course consists of fourteen lectures. Relevant material
(personal notes, scientific articles, all in English) for the lectures will be provided as needed using the Hoppii system. Part of the classes
will emphasize on problem-solving situations with guidance.

あり / Yes

なし / No

授業形態/methods of teaching：対面/face to face

※各回の授業形態は予定です。教員の指示に従ってください。

1[対面/face to face]：What is bioinformatics?
-Part 1

Why is bioinformatics so relevant nowadays? Introduction to
NCBI, Expasy, and other resource sites of bioinformatics.

2[対面/face to face]：What is
bioinformatics?
-Part 2

Understanding the span and imitations of bioinformatics. Pending issues.

3[対面/face to face]：What is Life? Living
organisms.

Introduction to basic concepts in biology. Chemistry of Life.

4[対面/face to face]：Rules of the Game.
Part 1

Variety of life forms. Basic concepts in molecular biology.

5[対面/face to face]：Rules of the Game.
Part 2

Basic concepts in molecular biology (continued).

6[対面/face to face]：Rules of the Game.
Part 3

Basic concepts in molecular biology (continued).
Terminology and processes.

7[対面/face to face]：Nucleotide
sequences. Part 1

Chemistry of DNA and RNA molecules (I).

8[対面/face to face]：Nucleotide
sequences. Part 2

Chemistry of DNA and RNA molecules (II).

9[対面/face to face]：Analyzing a protein
sequence. Part 1

Retrieval of a protein sequence.

10[対面/face to face]：Analyzing a protein sequence. Part 2

Pairwise and Multiple sequence alignment.
BLAST and Clustal Omega.
PAM and BLOSUM scoring systems.

11[対面/face to face]：Evolution and
phylogenetic trees. Part 1.

Biological basis of evolution and phylogenetics at
molecular level.

12[対面/face to face]：Evolution and
phylogenetic trees. Part 2.

Phylogenetic tree construction methods. Distance-based methods.

13[対面/face to face]：Evolution and
phylogenetic trees. Part 3.

Interpretation
of phylogenetic trees.

14[対面/face to face]：Role of Bioinformatics in the COVID-19 era.

A case study. How SARS-CoV-2 evolves and attempts to persist in our world.

Standard study time outside of class for preparation and review: approximately 5 hours. Please note that the first lectures are of introductory level.
During classes, a personal computer will be required to login and access database sites, retrieve specific information, or to perform computation. Also, you will be asked to work using specific analysis software (available from public servers) on relevant data, and interpret the obtained results.

"Bioinformatics for Dummies", J.-M. Claverie, C. Notredame,
Wiley Publishing Inc., 2007.
"Essential Bioinformatics", Jin Xiong, Cambridge University Press, 2006.
Purchase of these books is not necessary. Lectures are based on a collection of books and articles from several sources. Therefore, material (prints) will be provided. Information is widely available on the internet.

Relevant scientific articles will be provided prior or during classes. However, the scope of these will be tailored to the capabilities of the student.

Reports (20%) are to be submitted as requested within deadline
limit. Final exam (60%) at the end of course. Active participation in class (20%) is strongly encouraged, especially durinig discussion of topics. Some of the reports require the student to link to a server to retrieve data and perform the appropriate analysis.

Due to the manageable number or students in each session, a
one-on-one interaction during classes has been always possible.
This provides a real-time feedback to adjust the content of each lecture, to overcome the wide diversity of backgrounds of the students. In a such a way, this course, although introductory, can be offered to any student holding any background, and personal interest stands as the only requirement.

A personal computer with audiovisual capabilities, and internet access is highly recommended. All handouts, study material, assignments will be uploaded, and reports will be submitted via the Hoppii system.

None