Bioinformatics (MTAT.03.239)

Course info

• The first meeting will take place on February 15.
• Lectures: Thursday 14:15 - 16:00, J. Liivi 2 - 111
• Practice sessions: Thursday 16:15 - 18:00, J. Liivi 2 - 111
• Consultations: Monday 12:00-13:00 (J. Liivi 2 - 225) and Wednesday 16:00-17:00 (J. Liivi 2-611)
• Project selection: link
• BIIT (Bioinformatics, Algorithmics, and Data Mining group) group website : http://biit.cs.ut.ee/

Contacts

• Course forum: Piazza
• Homework submissions and grades: Gradeoscope (Entry Code: 93YNJG)
• Course materials: https://github.com/kauralasoo/MTAT.03.239_Bioinformatics
• Lecturer: Kaur Alasoo (kaur.alasoo [at] ut.ee)

Learning objectives:

• You will learn how to transfer the theoretical skills that you have learned in Data Mining, Neural Networks and Algorithmics courses to practical data analysis problems, with a particular focus on biology.
• You will know how to assess the quality of data via exploratory analysis (clustering, PCA) and know how to detect and when to remove outlier samples.
• You will understand the basic concepts of information flow in biological systems (genetic variant -> TF binding -> gene expression -> protein expression -> cellular phenotypes/imaging -> organismal phenotypes ) and what are the main biological and computational approaches to analyse it.

Grading and requirements:

The grade is calculated from the total number of points (max 100). The points can be earned as follows:

• Homeworks (50 points): there will be 10 homeworks, each worth 5 points;
• Group project and presentation at the poster session (20 points);
• Written exam (30 points);
• Additional points can be earned from bonus tasks within homeworks;
• Attending at least 8 out of 11 practice sessions is compulsory: after missing 3 practice sessions each additional missed practice session results in losing 5 points.

In order to pass the course the student must get at least 50% from homeworks (threshold 25 points), at least 50% from the project (threshold 10 points) and at least 50% from the exam (threshold 15 points).